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RegulationofGeneExpressioninEukaryotes

BIOL222

Ch.19

DifferentialGeneExpressioninEukaryotes

•  Cellsinamulticellulareukaryoticorganism

•  geneticallyidentical

•  differentialgeneexpression

•  Createsdifferencesbetweencelltypes

DNA

Signal

Gene

NUCLEUS

Chromatin modification

Chromatin

Gene available for transcription

Exon

Intron

Tail

RNA

Cap

RNA processing

Primary transcript

mRNA in nucleus

Transport to cytoplasm

mRNA in cytoplasm

Translation

CYTOPLASM

Degradation of mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transport to cellular destination

Degradation of protein

Transcription

RegulationofChromatinStructure

•  highlypackedheterochromatin

•  Genesareusuallynot

expressed

•  Chemicalmodificationstohistones

•  andDNAofchromatin

•  influencebothchromatin

structureandgeneexpression

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HistoneModifications•  histoneacetylation

•  acetylgroupsareattachedtopositivelychargedlysinesinhistonetails

•  loosenschromatinstructure

•  promotingtranscription

•  histonemethylation

•  cancondensechromatin

•  Cancauselongtermgeneinactivation

•  Leadingtoalteredcelldifferentiation

•  phosphorylationnexttoamethylatedaminoacid

•  canloosenchromatin

Histone tails

DNA double helix

(a) Histone tails protrude outward from a nucleosome

Acetylated histones

Amino acids available for chemical modification

(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

Unacetylated histones

EpigeneticInheritance

•  epigeneticinheritance

•  traitstransmittedbymechanismsnotdirectlyinvolvingthenucleotidesequence

•  Duetomethylation,acetylation,orphosphorylation

Enhancer (distal control elements)

Proximal control elements

Poly-A signal sequence

Termination region

Downstream Promoter Upstream DNA

Exon Exon Exon Intron Intron

Exon Exon Exon Intron Intron Cleaved 3ʹ end of primary transcript

Primary RNA transcript

Poly-A signal

Transcription

5 ́RNA processing

Intron RNA

Coding segment

mRNA

5ʹ Cap 5ʹ UTR Start

codon Stop

codon 3ʹ UTR Poly-A tail

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OrganizationofaTypicalEukaryoticGene•  controlelements

•  segmentsofnoncodingDNA

•  helpregulatetranscriptionbybindingcertainproteins

•  criticaltothepreciseregulationofgeneexpression

•  indifferentcelltypes

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•  Proximalcontrolelements

•  locatedclosetothe

promoter

•  Distalcontrolelements

•  enhancers

•  activator

•  bindstoanenhancer

•  stimulates

transcriptionofa

gene

EnhancersandSpecificTranscriptionFactors

Enhancer TATA box

Promoter Activators

DNA Gene

Distal control element

Group of mediator proteins

DNA-bending protein

General transcription factors

RNA polymerase II

RNA polymerase II

Transcription initiation complex RNA synthesis

PLAY

RNAProcessing

•  Post-transcriptionalcontrol

•  alternativeRNAsplicing

•  differentmRNA

molecules

•  fromthesame

primarytranscript

•  dependingon

whichexonsare

used

or

RNA splicing

mRNA

Primary RNA transcript

Troponin T gene

Exons

DNA

mRNADegradation

•  LifespanofmRNAmolecules

•  keytodeterminingprotein

synthesis

•  determinedinpartbysequencesin

theleaderandtrailerregions

•  EukaryoticmRNA

•  morelonglivedthanprokaryotic

mRNA

•  Methylatedcap,Poly-Atail

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ProteinProcessingandDegradation•  proteinprocessing

•  Thecleavageand/oradditionofchemicalgroups

•  subjecttocontrol

•  Proteasomes

•  giantproteincomplexes

•  bindproteinmoleculesanddegradethem

Proteasome and ubiquitin to be recycled Proteasome

Protein fragments (peptides) Protein entering a

proteasome

Ubiquitinated protein

Protein to be degraded

Ubiquitin

InitiationofTranslation•  Otherformsofregulationincluderegulationof…

•  theinitiationoftranslationofselectedmRNAs

•  canbeblockedbyregulatoryproteinsinthecytosol

•  thatbindtosequencesorstructuresofthemRNA

•  Alternatively,translationofallmRNAsinacellmayberegulatedsimultaneously

•  Ie.translationinitiationfactorsaresimultaneouslyactivated

•  inaneggfollowingfertilization

NoncodingRNAs

•  OnlyasmallfractionofDNAcodesforproteins,

rRNA,andtRNA

•  Asignificantamountofthegenome

•  maybetranscribedintononcodingRNAs

•  NoncodingRNAs

•  regulategeneexpressionattwopoints

•  chromatinconfiguration

•  mRNAtranslation

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MicroRNAsandSmallInterferingRNAs•  RNAinterference(RNAi)

•  ProcessofinhibitionofgeneexpressionbyRNAmolecules

•  causedbysmallinterferingRNAs(siRNAs)andmiRNA’s

•  MicroRNAs(miRNAs)

•  smallsingle-strandedRNA

molecules

•  bindtomRNA

•  candegrademRNAorblock

itstranslation

miRNA- protein complex (a) Primary miRNA transcript

Translation blocked

Hydrogen bond

(b) Generation and function of miRNAs

Hairpin miRNA

miRNA

Dicer

3ʹ

mRNA degraded

5ʹ

•  siRNAsandmiRNAs

•  similarbutformfromdifferentRNAprecursors

•  siRNAs

•  playaroleinheterochromatinformationbyfacilitatingmethylation

•  canblocklargeregionsofthechromosome

•  mayalsoblocktranscriptionofspecificgenes

MicroRNAsandSmallInterferingRNAs

DifferentialGeneExpressionandCellDifferentiation

•  embryonicdevelopment

•  fertilizedegggivesrisetomany

differentcelltypes

•  Celltypesareorganizedsuccessivelyinto

•  tissues,organs,organsystems,and

thewholeorganism

•  Geneexpressionorchestratesthe

developmentalprogramsofanimals

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•  Celldifferentiation

•  processbywhichcellsbecome

specializedinstructureandfunction

•  morphogenesis

•  physicalprocessesthatgivean

organismitsshape

•  Differentialgeneexpression

•  resultsfromgenesbeingregulated

differentlyineachcelltype

•  Materialsintheeggcansetupgene

regulationthatiscarriedoutascellsdivide

DifferentialGeneExpressionandCellDifferentiation

CytoplasmicDeterminants•  Anegg’scytoplasmcontains

•  RNA,proteins,andothersubstances

•  thataredistributedunevenlyintheunfertilizedegg

•  Cytoplasmicdeterminants

•  maternalsubstancesintheeggthatinfluenceearlydevelopment

•  Duringmitosis

•  cellscontaindifferentcytoplasmicdeterminants

•  leadstodifferentgeneexpression

(a) Cytoplasmic determinants in the egg

Two different cytoplasmic

determinants

Unfertilized egg cell

Sperm

Fertilization

Zygote

Mitotic cell division

Two-celled embryo

Nucleus

•  induction

•  Aprocesswheresignal

moleculesfromembryonic

cells

•  causetranscriptional

changesinnearbytarget

cells

•  Thus,interactionsbetweencells

inducedifferentiationofspecialized

celltypes

InductiveSignals

(b) Induction by nearby cells

Signal molecule (inducer)

Signal transduction

pathway

Early embryo (32 cells)

NUCLEUS

Signal receptor

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SequentialRegulationofGeneExpression

•  Determination

•  commitsacelltoitsfinal

fate

•  precedesdifferentiation

•  Celldifferentiationismarkedby

theproductionoftissue-specific

proteins

Embryonic precursor cell

Nucleus

OFF

DNA

Master regulatory gene myoD Other muscle-specific genes

OFF

OFF mRNA

MyoD protein (transcription

factor) Myoblast (determined)

mRNA mRNA mRNA mRNA

Myosin, other muscle proteins,

and cell cycle– blocking proteins Part of a muscle fiber

(fully differentiated cell)

MyoD Another transcription

factor

TypesofGenesAssociatedwithCancer•  Cancer

•  canbecausedbymutationstogenes

•  thatregulatecellgrowthanddivision

•  Tumorviruses

•  cancausecancerinanimalsincludinghumans

•  Oncogenes

•  cancer-causinggenes

•  Proto-oncogenes

•  correspondingnormalcellulargenes

•  responsiblefornormalcellgrowthanddivision

•  Conversionofaproto-oncogenetoanoncogene

•  canleadtoabnormalstimulationofthecellcycle

•  Proto-oncogenescanbeconvertedtooncogenesby

•  MovementofDNAwithinthegenome:ifitendsupnearanactivepromoter,transcriptionmayincrease

•  Amplificationofaproto-oncogene:increasesthenumberofcopiesofthegene

•  Pointmutationsintheproto-oncogeneoritscontrolelements:causesanincreaseingeneexpression

OncogenesandProto-Oncogenes

Normal growth- stimulating

protein in excess

New promoter

DNA

Proto-oncogene

Gene amplification: Translocation or transposition:

Normal growth-stimulating protein in excess

Normal growth- stimulating

protein in excess

Hyperactive or degradation-

resistant protein

Point mutation:

Oncogene Oncogene

within a control element within the gene

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Tumor-SuppressorGenes

•  Tumor-suppressorgenes

•  helppreventuncontrolledcellgrowth

•  Mutationsthatdecreaseproteinproductsoftumor-suppressorgenes

•  maycontributetocanceronset

•  Tumor-suppressorproteins

•  RepairdamagedDNA

•  Controlcelladhesion

•  Inhibitthecellcycleinthecell-signalingpathway

TheMultistepModelofCancerDevelopment•  Multiplemutationsneededforcancer

•  incidenceincreaseswithage

•  Acancerouscellischaracterizedbyatleastoneactiveoncogene

•  andthemutationofseveraltumor-suppressorgenes

EFFECTS OF MUTATIONS

Malignant tumor (carcinoma)

Colon

Colon wall Loss of tumor- suppressor gene

APC (or other)

Activation of ras oncogene

Loss of tumor-suppressor

gene DCC

Loss of tumor-suppressor

gene p53

Additional mutations

Larger benign growth (adenoma)

Small benign growth (polyp)

Normal colon epithelial cells

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3

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Youshouldnowbeableto:

1.  Explaintheconceptofanoperonandthefunctionoftheoperator,repressor,andcorepressor

2.  Explaintheadaptiveadvantageofgroupingbacterialgenesintoanoperon

3.  Explainhowrepressibleandinducibleoperonsdifferandhowthosedifferencesreflectdifferencesinthepathwaystheycontrol

4.  ExplainhowDNAmethylationandhistoneacetylationaffectchromatinstructureandtheregulationoftranscription

5.  Definecontrolelementsandexplainhowtheyinfluencetranscription

6.  Explaintheroleofpromoters,enhancers,activators,andrepressorsintranscriptioncontrol

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7.  Explainhoweukaryoticgenescanbecoordinatelyexpressed

8.  DescribetherolesplayedbysmallRNAsongeneexpression

9.  Explainwhydeterminationprecedesdifferentiation

10.  Describetwosourcesofinformationthatinstructacelltoexpressgenesattheappropriatetime

11.  Explainhowmutationsintumor-suppressorgenescancontributetocancer