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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
5
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
6
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
7
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
8
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