32 Gene regulation in Eukaryotes

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 in Prokaryotes and Eukarykotes

• Prokaryotes– Operons

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

not in operons)

– simultaneous transcription and translation

• Eukaryotes– No operons, but they still

need to coordinate regulation

– More kinds of control elements

– RNA processing– Chromatin remodeling

• Histones must be modified to loosen DNA

– Short- and long-term regulation

Figure 19.3

Signal

NUCLEUS

Chromatin modification:

Gene

DNA

RNATranscription

RNA processing

Transport to cytoplasmCYTOPLASM

Degradationof mRNA

Translation

Polypetide CleavageChemical modificationTransport to cellular destination

Active protein

Degradation of protein

Degraded protein

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

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 loosens DNA 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

Review transcription in Eukarkyotes

Enhancer(distal control elements)

Proximalcontrol elements

DNA

UpstreamPromoter

Exon Intron Exon Intron

Poly-A signalsequence

Exon

Terminationregion

Transcription

Downstream

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 components must be assembled to initiate transcription

Those common components are called “General Transcription Factors”

There are also many other transcription factors that control transcription of particular genes in particular conditions

Control of Galactose metabolism in yeast

Two Repressor proteins bind to control region

Control of Galactose metabolism in yeast

Galactose can bind to repressor complex. Opens activation site to stimulate transcription

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 enhancers affect 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 gene not expressed

Crystallin genenot expressed

Crystallin geneexpressed

Liver cell Lens cell

Fig 19.7

All cells have the same genes, but only certain genes are expressed in each tissue

Different set of activator proteins in the two cell types

Long-term control of transcription: methylation

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

histones, inactivating nearby genes

Genomic imprinting: inactivation of maternal or paternal genes

Some alleles are tagged by methyl C.

Signal

NUCLEUS

Chromatin modification:

Gene

DNA

RNATranscription

RNA processing

Transport to cytoplasmCYTOPLASM

Degradationof mRNA

Translation

Polypetide

Active protein

Degradation of protein

Degraded protein

Post-transcription control of gene expression

Alternative RNA splicingChromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Exons

DNA

PrimaryRNAtranscript

mRNA

RNA splicing or

Fig 19.8

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 cuts dsRNA into short segments

2 One strand of miRNA associates with protein.

3 The boundmiRNA can base-pair with any complementarymRNA

4Prevents geneexpresion

5

Fig 19.9

Degradation of a protein by a proteasome

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Ubiquitin

Protein tobe degraded

Ubiquinatedprotein

Proteasome

Proteasomeand ubiquitinto be recycled

Proteinfragments(peptides)

Ubiquitin molecules are attached to a protein

1 The ubiquitin-tagged protein is recognized by a proteasome.

2The proteasome cuts the protein into small peptides.

3

Protein entering aproteasome

Fig 19.10

Figure 21.1

Mutant Drosophila with an extra small eye on its

antenna

Development

DNA

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 from other cells activate a masterregulatory gene, myoD,

1

Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins.

2

 Determination and differentiation of muscle cells

Fig 21.10

The cell is now ireversibly determined

The cell is now fully differentiated

myoD is a “master control” gene: it makes a transcription factor that can activate other muscle specific genes.

The embryonic precursor cell is still undifferentiated

DNA

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 genesMaster control gene myoDNucleus

Determination. Signals from other cells activate a master regulatory gene, myoD,

1

Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins.

2

 Determination and differentiation of muscle cells

Fig 21.10The cell is now fully differentiated

The cell is now ireversibly determined to become a muscle cell.

DNA

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 genesMaster control gene myoDNucleus

Determination. Signals from other cells activate a masterregulatory gene, myoD,

1

Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins.

2

 Determination and differentiation of muscle cells

Fig 21.10

The cell is now ireversibly determined

The cell is now fully differentiated

Genetic control of Flower Development

ApetalaClass A

AgamousClass C

PistillataClass B

“ABC Model”

These genes all code for transcription factors

Normal Flower

The effect of the bicoid gene, an egg-polarity gene in Drosophila

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

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

• Regulatory genes that control organ identity

• Conserved from flies to mammals

Homeotic genes