Exam #2 W 7/9 in class Today: Development and Genome Organization.

109
am #2 W 7/9 in class Today: Development and Genome Organization

TAGS:

Transcript of Exam #2 W 7/9 in class Today: Development and Genome Organization.

Page 1: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Exam 2 W 79 in class

Today Development and Genome Organization

Development differentiating cells to become an organism

Cells function differently because they express differentgenes

The proper control of gene expression is critical for proper development

So development in animals is one way

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 2: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Development differentiating cells to become an organism

Cells function differently because they express differentgenes

The proper control of gene expression is critical for proper development

So development in animals is one way

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 3: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Cells function differently because they express differentgenes

The proper control of gene expression is critical for proper development

So development in animals is one way

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 4: Exam #2 W 7/9 in class Today: Development and Genome Organization.

The proper control of gene expression is critical for proper development

So development in animals is one way

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 5: Exam #2 W 7/9 in class Today: Development and Genome Organization.

So development in animals is one way

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 6: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Inverse relationship between smoking and weight more smoking less weight

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 7: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Effect of smoking on fetal development and how that can affect adults

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 8: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Adults exposed to smoke as fetuses have higher risk of obesity and heart disease

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 9: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What is the connection

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 10: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Obesity Diabetes Heart Disease High Blood Pressure Some Cancers all may have some origins during fetal development

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 11: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Adults metabolism may react to poor nutrition as fetuseshellip

Adaptation of Thriftiness

or

Catch Up Growth

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 12: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 13: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 14: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Adults metabolism may react to poor nutrition as fetuseshellipAdaptation of Thriftiness or Catch Up Growth

Study of babies born during Dutch famine of 1944-45hellip

20 years later found that these babies had higher rates of obesity

Precise mechanism is not known

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 15: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 16: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 17: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

For Momrsquos who abstained during pregnancy no effect on fetus or as adult

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 18: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

17000 births studied and checked at age 16 and 33

Fetuses exposed to smoking had increased rate of obesity and more smoking meant more obesity

Smoking during first trimester had same effect as during whole pregnancy

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 19: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

For diabetes more than 10 cigarettes per day gave a 4 times greater risk of diabetes

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 20: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What about smoking

Risk of high blood pressure also increases with increased exposure to fetus of smoking during pregnancy

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 21: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 22: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

Nicotine can inhibit hunger and increase energy expenditure

This can lead to poor fetal nutrition

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 23: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 24: Exam #2 W 7/9 in class Today: Development and Genome Organization.

AAL 388

Mammalian circulation

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 25: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Nicotine causes blood vessels to constrict

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 26: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

CO in blood decreases delivery of O2 to fetus

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 27: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

These are all indirect affects leading to ldquoadaptation to thriftinessrdquohellip

Nicotine can inhibit hunger and increase energy expenditure

Nicotine causes constriction of blood vessels and may limit blood flow to the fetus

CO in blood decreases delivery of O2 to fetus

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 28: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 29: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Hormones are molecules produced in one cell and signal another

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 30: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why

Nicotine and other toxins in smoke may directly affect hormones that direct fetal development

Including hormones that direct brain development

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 31: Exam #2 W 7/9 in class Today: Development and Genome Organization.

So

Smoking during pregnancy may have indirect andor direct affects on fetal development and these affects may manifest themselves in adults

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 32: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Correlation of weight (BMI)

Identical twins reared together 80

Identical twins reared apart 72

Fraternal twins reared together 43

Biological siblings 34

Parents and children living together 26

Adopted children and parents 4

Unrelated children living together 1

Correlation of weight and relatedness

The nature of environmental influences on weight and obesity A behavior genetic analysis Grilo Carlos M Pogue-Geile Michael F Psychological Bulletin Vol 110(3) Nov 1991 pp 520-537 And two books by Matt Ridley Nature via Nurture (2003) and Genome the Autobiography of a Species in 23 Chapters (1999)

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 33: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Nature and Nurture

Are traits coded for by genes fixed while traits coded for by the environment are under our control

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 34: Exam #2 W 7/9 in class Today: Development and Genome Organization.

So development in animals is one way

Why

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 35: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Fig 233

Developmental mutants of Drosophila melanogaster

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 36: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Vertebrate Development

from zygote to adult

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 37: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Early embryo developmentFig 1913

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 38: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Totipotent ability to differentiate into any cell-type

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 39: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Totipotency is limited to early stages of animal development

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 40: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why do cells lose totipotency

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 41: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why do cells lose totipotency

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 42: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Mature differentiated plant cells are totipotent

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 43: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why do cells lose totipotency

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 44: Exam #2 W 7/9 in class Today: Development and Genome Organization.

bullGene expression can be controlled at many points between DNA and making the final proteins

bullChanges in the various steps of gene expression control when and how much of a product are produced

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 45: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 46: Exam #2 W 7/9 in class Today: Development and Genome Organization.

DNA packaging fluctuateshellipgenes being expressed are unpackaged genes not needed are tightly packaged

Fig 1021

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 47: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Normally DNA is loosely packaged

During mitosis DNA is tightly packaged as chromosomes and

individually visible

Fig 38

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 48: Exam #2 W 7/9 in class Today: Development and Genome Organization.

DNA packaging fluctuateshellipSome of the tight packaging of DNA is irreversible

Fig 1021

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 49: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Irreversible packaging of DNA partially explains the loss of totipotency

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 50: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Stem cells still have totipotencyFig 1913

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 51: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Embryonic Stem Cells are totipotent

Adult Stem Cells are pluripotent (only form some cell types)

Fig 1914

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 52: Exam #2 W 7/9 in class Today: Development and Genome Organization.

What genetic mechanisms regulateallow development

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 53: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Increases in cell number play a

rolehellip

Fig 231

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 54: Exam #2 W 7/9 in class Today: Development and Genome Organization.

hellipso does cell death

Fig 231

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 55: Exam #2 W 7/9 in class Today: Development and Genome Organization.

CB 2119

Development of a mouse paw yellow areas show dying cells

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 56: Exam #2 W 7/9 in class Today: Development and Genome Organization.

All humans are female for the first nine weeks of development

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 57: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Fig 2327

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 58: Exam #2 W 7/9 in class Today: Development and Genome Organization.

All humans are female for

the first nine weeks of

development

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 59: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 60: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Each whorl expresses a specific combination of three genes

Fig 2324

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 61: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Fig 2323

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 62: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Changing expression of A B or C genes

changes organ identity

Fig 2324

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 63: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Flower partsComplexity from a few simple genes

4 whorls of a flowerFig 2323

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 64: Exam #2 W 7/9 in class Today: Development and Genome Organization.

How does a cell know where it is

Fig 232

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 65: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Drosophila Development

Fig 234

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 66: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Polarity development by mRNA localization

Fig 235

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 67: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Hox genes regulate the identity of body parts Fig 2311

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 68: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Expression of hox genes in the embryo give rise to different adult body parts

embryo

adult

Fig 2311

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 69: Exam #2 W 7/9 in class Today: Development and Genome Organization.

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 70: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Drosophila and vertebrate Hox protein show striking similarities (500 million years since common ancestor)

Fig 2316

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 71: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Many hox proteins have common sequences(these are from Drosophila)

Fig 2313

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 72: Exam #2 W 7/9 in class Today: Development and Genome Organization.

helix-turn-helix a common DNA-binding motif

Fig 2313

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 73: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Many developmental genes are transcription factors

these are from Drosophila

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 74: Exam #2 W 7/9 in class Today: Development and Genome Organization.

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 75: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Reporter gene

protein

coding region

promoter reporter gene (luciferase etc)

easily visualized protein

promoter

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1219

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 76: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Interaction of genes can set gradients in cellsorganisms that signal how different regions should develop

ldquoIntroduction to Genetic Analysisrdquo 9th ed copy2008 by Griffiths et al Fig 1218

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 77: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Why change gene expressionbullDifferent cells need different componentsbullResponding to the environmentbullReplacement of damagedworn-out parts

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 78: Exam #2 W 7/9 in class Today: Development and Genome Organization.

The order of Hox genes parallels the order of body parts in which they are expressed

Fig 2317

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 79: Exam #2 W 7/9 in class Today: Development and Genome Organization.

25000 12

How are genomes organized Tbl 202

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 80: Exam #2 W 7/9 in class Today: Development and Genome Organization.

httpwwwncbinlmnihgovmapviewmapscgiORG=humanampCHR=XampMAPS=ideogr[XpterXqter]genes[10015369239100]

Map of human chromosome 20

How does the organization of a genome affect its function

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 81: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Figure 7-113 Molecular Biology of the Cell 4th ed by Alberts et al(Adapted from S Baxendale et al Nat Genet 1067ndash76 1995)

Comparison of Fugu and human huntingtin gene

75 X bigger

both have 67 exons connected by lines

(green indicates transposons prevalent in human version)

(puffer fish)

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 82: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Some genes have several similar sequences within the genome known as a gene family

Fig 87

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 83: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Hemoglobin (carries O2 in the blood) is comprised of a gene family in humans

Fig 87

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 84: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Different members of the hemoglobin gene family are expressed at different developmental stages

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 85: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Fetal Hb binds O2 more strongly than maternal Hb

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 86: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Pseudogenes have the structure of a gene but are not expressed

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 87: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Most cells in an organism have the same DNAWhich cells have different DNA

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 88: Exam #2 W 7/9 in class Today: Development and Genome Organization.

DNA is rearranged in B-cells during antibody production

Fig 179

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 89: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Each B-cell produces a unique antibody

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 90: Exam #2 W 7/9 in class Today: Development and Genome Organization.

DNA rearrangements in B-cells allow each B-cell to produce a unique antibody

Fig 179

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 91: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679andWhich transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 92: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Transposons mobile DNA

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 93: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Transposons comprise much of human DNA

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 94: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Fig 1712C

Retro-transposons move via an RNA intermediate

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 95: Exam #2 W 7/9 in class Today: Development and Genome Organization.

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Tbl 1 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 96: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Humans and chimpanzees shared a common ancestor about 6 million years ago

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 97: Exam #2 W 7/9 in class Today: Development and Genome Organization.

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

human

chimp

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Humans have more transposons than chimps

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 98: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 99: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

What affect do transposons have in humans

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 100: Exam #2 W 7/9 in class Today: Development and Genome Organization.

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Fig 3 Recently Mobilized Transposons in the Human and Chimpanzee Genomes (2006) Ryan E Mills et al The American Journal of Human Genetics 78 671-679

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 101: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Does transposition cause disease

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 102: Exam #2 W 7/9 in class Today: Development and Genome Organization.

An active copy of the L1 transposon lsquojumpedrsquo into the factor VIII gene and caused hemophilia

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 103: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Diseases caused by transposon insertion

bullDuchenne muscular dystrophy

bullCoffin-Lowry syndrome

bullFukuyama-type congenital muscular dystrophy (FCMD)

bullcolon cancer

bullchronic granulomatous disease

bullX-linked dilated cardiomyopathy

bullfamilial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

bullneurofibromatosis type 1

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 104: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Active human transposons have been estimated to generate about one new insertion per 10ndash100 live births

Which transposons are mobile

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 105: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Tbl 1 Which transposable elements are active in the human genome (2007) Ryan E Mills et al Trends in Genetics 23 183-191

Which transposons are mobile

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 106: Exam #2 W 7/9 in class Today: Development and Genome Organization.

QuickTimetrade and aTIFF (Uncompressed) decompressor

are needed to see this picture

Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans For example over 600 recent transposon insertions were identified by examining DNA resequencing traces from 36 genetically diverse humans

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 107: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Conclusions

bullTransposons may play a role in evolution

bullMore abundant transposons in humans show ldquorecentrdquo transposon activity

bullTransposons are still active and can cause mutations and disease

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109
Page 108: Exam #2 W 7/9 in class Today: Development and Genome Organization.

Exam 2 W 79 in class

  • PowerPoint Presentation
  • Slide 2
  • Slide 3
  • Slide 4
  • Slide 5
  • Slide 6
  • Slide 7
  • Slide 8
  • Slide 9
  • Slide 10
  • Slide 11
  • Slide 12
  • Slide 13
  • Slide 14
  • Slide 15
  • Slide 16
  • Slide 17
  • Slide 18
  • Slide 19
  • Slide 20
  • Slide 21
  • Slide 22
  • Slide 23
  • Slide 24
  • Slide 25
  • Slide 26
  • Slide 27
  • Slide 28
  • Slide 29
  • Slide 30
  • Slide 31
  • Slide 32
  • Slide 33
  • Slide 34
  • Slide 35
  • Slide 36
  • Slide 37
  • Slide 38
  • Slide 39
  • Slide 40
  • Slide 41
  • Slide 42
  • Slide 43
  • Slide 44
  • Slide 45
  • Slide 46
  • Slide 47
  • Slide 48
  • Slide 49
  • Slide 50
  • Slide 51
  • Slide 52
  • Slide 53
  • Slide 54
  • Slide 55
  • Slide 56
  • Slide 57
  • Slide 58
  • Slide 59
  • Slide 60
  • Slide 61
  • Slide 62
  • Slide 63
  • Slide 64
  • Slide 65
  • Slide 66
  • Slide 67
  • Slide 68
  • Slide 69
  • Slide 70
  • Slide 71
  • Slide 72
  • Slide 73
  • Slide 74
  • Slide 75
  • Slide 76
  • Slide 77
  • Slide 78
  • Slide 79
  • Slide 80
  • Slide 81
  • Slide 82
  • Slide 83
  • Slide 84
  • Slide 85
  • Slide 86
  • Slide 87
  • Slide 88
  • Slide 89
  • Slide 90
  • Slide 91
  • Slide 92
  • Slide 93
  • Slide 94
  • Slide 95
  • Slide 96
  • Slide 97
  • Slide 98
  • Slide 99
  • Slide 100
  • Slide 101
  • Slide 102
  • Slide 103
  • Slide 104
  • Slide 105
  • Slide 106
  • Slide 107
  • Slide 108
  • Slide 109

Today ’ s Lecture Topics Whole genome sequencing Shotgun sequencing method

Today ’ s Lecture Topics Whole genome sequencing Shotgun sequencing method

Announcements We are finishing Chapter 11 today We are finishing Chapter 11 today See me after class to pick up your graded exam if you took a makeup exam.

Announcements We are finishing Chapter 11 today We are finishing Chapter 11 today See me after class to pick up your graded exam if you took a makeup exam.

Genome Assembly Strategies - VBC | Victorian ... Assembly Strategies... · Genome Assembly Strategies Yesterday, today, ... E.coli 4.6 Mbp ... – Analyse/simplify/clean the overlap

Genome Assembly Strategies - VBC | Victorian ... Assembly Strategies... · Genome Assembly Strategies Yesterday, today, ... E.coli 4.6 Mbp ... – Analyse/simplify/clean the overlap

Schedule Today and Wednesday: Lecture Monday, 4/08: Exam 1.

Schedule Today and Wednesday: Lecture Monday, 4/08: Exam 1.

Molecular Techniques II. Today: Advanced PCR Techniques Other Amplification Technologies Primer/Probe Design Whole Genome/Transcriptome Amplification.

Molecular Techniques II. Today: Advanced PCR Techniques Other Amplification Technologies Primer/Probe Design Whole Genome/Transcriptome Amplification.

Class Review and Sample Exam Questions CSE 237AClass Overview • Plan for today: –Class review and sample questions from previous exams • Upcoming: –HW3 due today –Exam the

Class Review and Sample Exam Questions CSE 237AClass Overview • Plan for today: –Class review and sample questions from previous exams • Upcoming: –HW3 due today –Exam the

Today: Quizz 8 Friday: GLM review Monday: Exam 2.

Today: Quizz 8 Friday: GLM review Monday: Exam 2.

Today: Patenting Life *Exam #2 Th 3/26 Monsanto Stock price .

Today: Patenting Life *Exam #2 Th 3/26 Monsanto Stock price .

Human Genome Case Study - USA Today

Human Genome Case Study - USA Today

CS/ECE 252 Exam 4 Reviewpages.cs.wisc.edu/.../2015fallReviewSessions/exam4reviewWorksheetQuestions.pdfExam 4 on Monday, December 14th, during class Today: Exam 4 Review ... Moore’s

CS/ECE 252 Exam 4 Reviewpages.cs.wisc.edu/.../2015fallReviewSessions/exam4reviewWorksheetQuestions.pdfExam 4 on Monday, December 14th, during class Today: Exam 4 Review ... Moore’s

MID TERM EXAM 1 WEEK FROM TODAY kmw

MID TERM EXAM 1 WEEK FROM TODAY kmw

Uncertain Times to Today US History and Government NY State Regents Exam Review.

Uncertain Times to Today US History and Government NY State Regents Exam Review.

Today – Exam#3 Review Final Examsherrill/isp209f5/lectures/... · 2005. 12. 6. · Today – Exam#3 Review • Exam #3 is Thursday December 8th in this room, BPS 1410 • The exam

Today – Exam#3 Review Final Examsherrill/isp209f5/lectures/... · 2005. 12. 6. · Today – Exam#3 Review • Exam #3 is Thursday December 8th in this room, BPS 1410 • The exam

Today – Exam#2 Reviebogner/isp209s2010/lectures/exam2Review.pdf · ISP209s10 Exam2 Review -1-Today – Exam#2 Review •Exam #2 is Tuesday 3/30 •The exam is 40 multiple choice

Today – Exam#2 Reviebogner/isp209s2010/lectures/exam2Review.pdf · ISP209s10 Exam2 Review -1-Today – Exam#2 Review •Exam #2 is Tuesday 3/30 •The exam is 40 multiple choice

LAST EXAM-TIPS WORKSHOP TODAY @12:30 in F309

LAST EXAM-TIPS WORKSHOP TODAY @12:30 in F309

Today: Genetic Technology Wrap-up Exam Review Remember: Final Exam is Wednesday, 12/13 at 1 pm!

Today: Genetic Technology Wrap-up Exam Review Remember: Final Exam is Wednesday, 12/13 at 1 pm!

International Wheat genome Sequencing Consortium · The International Wheat Genome Sequencing Consortium (IWGSC) published today in the international journal Science a draft sequence

International Wheat genome Sequencing Consortium · The International Wheat Genome Sequencing Consortium (IWGSC) published today in the international journal Science a draft sequence

Genome Replication -- Genom - Welcome to Telostep | TELOSTEP 13... · understanding the details of eukaryotic genome replication. This work is ongoing, with research today centered

Genome Replication -- Genom - Welcome to Telostep | TELOSTEP 13... · understanding the details of eukaryotic genome replication. This work is ongoing, with research today centered

New Today – Exam#2 Review Energy, Work, etc. · 2010. 3. 25. · ISP209s10 Exam2 Review -1-Today – Exam#2 Review •Exam #2 is Tuesday 3/30 •The exam is 40 multiple choice questions.

New Today – Exam#2 Review Energy, Work, etc. · 2010. 3. 25. · ISP209s10 Exam2 Review -1-Today – Exam#2 Review •Exam #2 is Tuesday 3/30 •The exam is 40 multiple choice questions.

Schedule Your Yearly Eye Exam TODAY! Sports Vision ... · 2/10/2016  · Issue 10, Feb. 2016 Don’t Take Your Eyesight For Granted! Schedule Your Yearly Eye Exam TODAY! 1 st Eye

Schedule Your Yearly Eye Exam TODAY! Sports Vision ... · 2/10/2016  · Issue 10, Feb. 2016 Don’t Take Your Eyesight For Granted! Schedule Your Yearly Eye Exam TODAY! 1 st Eye