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32 Gene regulation inEukaryotes Lecture Outline 11/28/05

• Gene regulation in eukaryotes– Chromatin remodeling– More kinds of control elements

• Promoters, Enhancers, and Silencers• Combinatorial control• Cell-specific transcription

– Post transcription gene regulation• mRNA processing• Micro RNAs• Protein degradation

– Differentiation and Development• A cascade of transcription regulators• Examples from flowers and fruit flies

Gene Regulation inProkaryotes and Eukarykotes

• Prokaryotes– Operons

• 27% of E. coli genes• (Housekeeping genes

not in operons)

– simultaneoustranscription andtranslation

• Eukaryotes– No operons, but they still

need to coordinateregulation

– More kinds of controlelements

– RNA processing– Chromatin remodeling

• Histones must be modifiedto loosen DNA

– Short- and long-termregulation Figure 19.3

Signal

NUCLEUS

Chromatinmodification:

Gene

DNA

RNATranscription

RNA processing

Transport to cytoplasmCYTOPLASM

Degradationof mRNA

Translation

Polypetide CleavageChemical modificationTransport to cellular destination

Active protein

Degradation of protein

Degraded protein

2

Nucleosome

30 nm

(b) 30-nm fiber

DNA Packing

Protein scaffold

300 nm

(c) Looped domains (300-nm fiber)

Loops

Scaffold

700 nm

1,400 nm

(d) Metaphase chromosome

Figure 19.2

Histone Modification

Figure 19.4a

Chromatin changes

Transcription

RNA processing

mRNA degradation

Translation

Protein processingand degradation

DNAdouble helix Amino acids

availablefor chemicalmodification

Histonetails

Histone acetylation loosensDNA to allow transcription

Figure 19.4 b

Unacetylated histones Acetylated histones

Activator recruits chromatin remodeling and acetylation proteins

http://cats.med.uvm.edu

Densely packed chromatin

Transcription

RNA Pol

3

Review transcription inEukarkyotes

Enhancer(distal control elements)

Proximalcontrol elements

DNA

UpstreamPromoter

Exon Intron Exon Intron

Poly-A signalsequence

Exon

Terminationregion

TranscriptionDownstream

Poly-Asignal

ExonIntronExonIntronExonPrimary RNAtranscript(pre-mRNA)

5′

Intron RNA

RNA processing:Cap and tail added;introns excised andexons spliced together

Coding segment

P P PGmRNA

5′ Cap 5′ UTR(untranslated

region)

Startcodon

Stopcodon

3′ UTR(untranslatedregion)

Poly-Atail

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Cleared 3′ endof primarytransport

Many componentsmust be assembled toinitiate transcription

Those commoncomponents are called“General TranscriptionFactors”

There are also many othertranscription factors that controltranscription of particular genes inparticular conditions

Control of Galactosemetabolism in yeast

Two Repressor proteins bind tocontrol region

Control of Galactosemetabolism in yeast

Galactose can bind to repressorcomplex. Opens activation siteto stimulate transcription

4

Distal controlelement

Activators

Enhancer

PromoterGene

TATAbox General

transcriptionfactors

DNA-bendingprotein

Group ofMediator proteins

RNAPolymerase II

RNAPolymerase II

RNA synthesisTranscriptionInitiation complex

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

A DNA-bending proteinbrings the bound activators

closer to the promoter.

2

Activator proteins bindto distal control elements.

1

The activators bind tocertain general transcription

factors and mediatorproteins.

3

Enhancers and activators

Fig 19.5

Transcriptional synergy

• Combinations of different enhancersaffect the strength of transcription

How eukaryotic gene repressors can function: Cell type–specific transcriptionEnhancer Promoter

Controlelements

Albumin gene

Crystallin gene

Liver cellnucleus

Lens cellnucleus

Albumin geneexpressed

Albumin genenot expressed

Crystallin genenot expressed

Crystallin geneexpressed

Liver cell Lens cell

Fig 19.7

All cells have thesame genes, butonly certaingenes areexpressed ineach tissue

Different set ofactivator proteinsin the two celltypes

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Long-term control of transcription:methylation

• Certain cytosine bases can bemethylated, which blocks transcription– Usually CG dinucleotides– Recruits proteins which deacetylate

histones, inactivating nearby genes

Genomic imprinting:inactivation of maternal or paternal genes

Somealleles aretagged bymethyl C.

Signal

NUCLEUS

Chromatinmodification:

Gene

DNA

RNATranscription

RNA processing

Transport to cytoplasmCYTOPLASM

Degradationof mRNA

Translation

Polypetide

Active protein

Degradation of protein

Degraded protein

Post-transcriptioncontrol of geneexpression

Alternative RNA splicingChromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Exons

DNA

PrimaryRNAtranscript

mRNA

RNA splicing or

Fig 19.8

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Micro-RNAs

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Degradation of mRNAOR

Blockage of translation

Target mRNAmiRNA

Proteincomplex

Dicer

Hydrogenbond

The micro-RNA (miRNA)precursor foldsback on itself

1 Dicer cutsdsRNA intoshort segments

2 One strandof miRNAassociates withprotein.

3 The boundmiRNA can base-pair with anycomplementarymRNA

4Prevents geneexpresion

5

Fig 19.9

Degradation of a protein by aproteasome

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Ubiquitin

Protein tobe degraded

Ubiquinatedprotein

Proteasome

Proteasomeand ubiquitinto be recycled

Proteinfragments(peptides)

Ubiquitin moleculesare attached to aprotein

1 The ubiquitin-taggedprotein is recognizedby a proteasome.

2The proteasomecuts the protein intosmall peptides.

3

Protein entering aproteasome

Fig 19.10

Figure 21.1

Mutant Drosophila with anextra small eye on its

antenna

DevelopmentDNA

OFF OFF

OFFmRNA

mRNA mRNA mRNA mRNA

Anothertranscriptionfactor

MyoDMuscle cell(fully differentiated)

MyoD protein(transcription factor)

Myoblast (determined)

Embryonicprecursor cell

Myosin, othermuscle proteins,and cell-cycleblocking proteins

Other muscle-specific genesmyoDNucleus

Determination. Signals fromother cells activate a masterregulatory gene, myoD,

1

Differentiation. MyoDprotein activatesother muscle-specifictranscription factors, whichin turn activate genes formuscle proteins.

2

Determination and differentiation of muscle cells

Fig 21.10

The cell is nowireversiblydetermined

The cell is now fullydifferentiated

myoD is a “master control” gene: it makes atranscription factor that can activate othermuscle specific genes.

The embryonic precursorcell is still undifferentiated

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DNAOFF OFF

OFFmRNA

mRNA mRNA mRNA mRNA

Anothertranscriptionfactor

MyoDMuscle cell(fully differentiated)

MyoD protein(transcription factor)

Myoblast (determined)

Embryonicprecursor cell

Myosin, othermuscle proteins,and cell-cycleblocking proteins

Other muscle-specific genesMaster control gene myoDNucleus

Determination.Signals from othercells activate amaster regulatorygene, myoD,

1

Differentiation. MyoDprotein activatesother muscle-specifictranscription factors, whichin turn activate genes formuscle proteins.

2

Determination and differentiation of muscle cells

Fig 21.10The cell is now fullydifferentiated

The cell is nowireversiblydetermined tobecome amuscle cell.

DNAOFF OFF

OFFmRNA

mRNA mRNA mRNA mRNA

Anothertranscriptionfactor

MyoDMuscle cell(fully differentiated)

MyoD protein(transcription factor)

Myoblast (determined)

Embryonicprecursor cell

Myosin, othermuscle proteins,and cell-cycleblocking proteins

Other muscle-specific genesMaster control gene myoDNucleus

Determination. Signals fromother cells activate a masterregulatory gene, myoD,

1

Differentiation. MyoDprotein activatesother muscle-specifictranscription factors, whichin turn activate genes formuscle proteins.

2

Determination and differentiation of muscle cells

Fig 21.10

The cell is nowireversiblydetermined

The cell is now fullydifferentiated

Genetic control of FlowerDevelopment

ApetalaClass A

AgamousClass C

PistillataClass B

“ABC Model”

These genes all code for transcription factors

NormalFlower

The effect of the bicoid gene, an egg-polarity gene inDrosophila

Tail

Head

Normal larva

Tail Tail

Mutant larva (bicoid)

A mutation in bicoid leads to tail structures at both ends(bottom larva).

T1 T2T3

A1 A2 A3 A4 A5 A6 A7A8

A8A7 A6 A7

A8

Figure 21.14

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Hierarchy of Gene Activity in Early Drosophila Development

Maternal effect genes (egg-polarity genes)

Gap genes

Pair-rule genes

Segment polarity genes

Homeotic genes of the embryo

Other genes of the embryo

Segmentation genesof the embryo

Drosophila pattern formation

Translation of bicoid mRNAFertilization

Nurse cells Egg cell

bicoid mRNA

Developing egg cell

Bicoid mRNA in mature unfertilized egg

100 µm

Bicoid protein inearly embryo

Anterior end

(b) Gradients of bicoid mRNA and bicoid protein in normal egg and early embryo.

1

2

3

Homeotic genes

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• Regulatorygenes thatcontrol organidentity

• Conservedfrom flies tomammals

Homeotic genes