GENOMICS

AP Biology Chap 21

• Genomes – set of genes and their interactions

• Bioinformatics – computational methods of gene analysis

- NCBI National Center Biotechnology

Information – database of DNA

sequences and proteins (proteomes)

NCBI HomePage

• The most ambitious mapping project to date has been the sequencing of the human genome

• Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003

• The project had three stages:

– Genetic (or linkage) mapping

– Physical mapping

– DNA sequencing

Fig. 21-2-4

Cytogenetic map

Genes locatedby FISH

Chromosomebands

Linkage mapping1

2

3

Geneticmarkers

Physical mapping

Overlappingfragments

DNA sequencing

Fluorescence In Situ Hybridization

• A linkage map (genetic map) maps the location of several thousand genetic markers on each chromosome

• A genetic marker is a gene or other identifiable DNA sequence

• Recombination frequencies are used to determine the order and relative distances between genetic markers

Fig. 21-3-3

Cut the DNAinto overlappingfragments short enoughfor sequencing

1

2

3

4

Clone the fragmentsin plasmid or phagevectors.

Sequence eachfragment.

Order thesequences intoone overallsequencewith computer software.

• A complete haploid set of human chromosomes consists of 3.2 billion base pairs

By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants

What do we know?

• Humans have 20,488 genes• With alternate gene splicing, we can

make 75,000 polypeptides• Genomes of most bacteria and

archaea range from 1 to 6 million base pairs (Mb); genomes of eukaryotes are usually larger

• Free-living bacteria and archaea have 1,500 to 7,500 genes

• Unicellular fungi have from about 5,000 genes and multicellular eukaryotes from 40,000 genes

• Number of genes is not correlated to genome size

• Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA

Table 21-1

About the human genome…

Only 1.5% codes for proteins, rRNA and tRNA

The rest is used for • regulatory sequences and introns

24% • pseudogenes (nonfunctioning

genes) 15% • repetitive DNA 59%

Fig. 21-7Exons (regions of genes coding for protein

or giving rise to rRNA or tRNA) (1.5%)

RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)

Introns andregulatorysequences(24%)

UniquenoncodingDNA (15%)

RepetitiveDNAunrelated totransposableelements (15%)

L1sequences(17%)

Alu elements(10%)

Simple sequenceDNA (3%)

Large-segmentduplications (5–6%)

Repetitive DNA

• 44% transposable elements (jumping genes)

- Transposons - cut and paste (ex Alu in primates)

- Most of these are retrotransposons – cut, copy to RNA, RT to DNA, and

paste (ex Line1 or L1)

• 15% – large segment and simple sequence DNA

- small ones STR - Short Tandem Repeats often used in centromeres and telomeres

Fig. 21-9

TransposonNew copy of transposon

Insertion

Transposonis copied

Mobile transposon

DNA ofgenome

(a) Transposon movement (“copy-and-paste” mechanism)

RetrotransposonNew copy of

retrotransposon

Insertion

Reversetranscriptase

RNA

(b) Retrotransposon movement

Animation Quiz 5 - Transposons: Shifting Segments of the Genome

“Jumping Genes”

The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn

Fig. 21-8

Genes

• Many eukaryotic genes are present in one copy per haploid set of chromosomes

• More than ½ occur in multigene families – such as for RNA products and hemoglobin

Fig. 21-10

DNARNA transcripts

Nontranscribedspacer Transcription unit

18S

28S

5.8S 28S

5.8S

rRNA

18S

DNA

(a) Part of the ribosomal RNA gene family

Heme

Hemoglobin

-Globin

-Globin

-Globin gene family -Globin gene family

Chromosome 16 Chromosome 11

2

12 1

G A

AdultFetusEmbryoFetus

and adultEmbryo

(b) The human -globin and -globin gene families

Genomic Evolution

• Duplication of chromosome sets (polyploidy)

• Chromosome alteration – duplications, inversions

• Exon shuffling

• Transposons

• Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs

• Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line

Why weAre

Smarter!

• The rate of duplications and inversions seems to have accelerated about 100 million years ago

• This coincides with when large dinosaurs went extinct and mammals diversified

How transposons affect genomes

• Multiple copies may facilitate crossing-over

• Insertion may block protein sequence

• Insertion may affect promoters

• Insertion may carry new genes to an area

• May create new sites for alternative splicing in RNA

Fig. 21-12

Transposableelement

Gene

Nonsisterchromatids

Crossover

Incorrect pairingof two homologsduring meiosis

and

Comparing evolutionary developmental processes

“evo-devo”

• Homeobox – 180 nucleotides that regulate gene expression during development

• Found in many organisms, both inverts and verts

• Called “hox genes” in mammals

• You should read “Our Inner Fish”!

Fig. 21-17

Adultfruit fly

Fruit fly embryo(10 hours)

Flychromosome

Mousechromosomes

Mouse embryo(12 days)

Adult mouse

• Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form.

• For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects

for example, flies with feet in place of antennae.