Control of eukaryotic gene expression
• As usual, much more complicated than in
prokaryotes.
– Increased amount of DNA
– Tight packing into nucleosomes
– Physical separation between nucleus & ribosomes
– mRNA processing and different life span
– Multicellular w/ development & differentiation
• Many options for control
– From DNA rearrangements to protein modification
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Overview of critical elements
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• DNA regions
– Promoter: TATA, CAAT, & GCG boxes
• RNA polymerase binds, with assistance.
– Enhancers and silencers: short sequences that
proteins bind to that influence transcription.
• Proteins
– TFIID: made of TBP (TATA box binding protein) and
about 12 TAFs (TBP associated factors).
– Transcription factors: basal and enhancer binding
– RNA polymerase II (for mRNA)
The Process of Transcription
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• Promoter recognition: 2 consensus sequences
– The -10 region: TATAAT (10 bases upstream from
where transcription actually starts.
– The -35 region, farther upstream, also important.
– “Consensus” sequence meaning the DNA sequence
from many genes averages out to this.
– The closer these 2 regions actually are to the
consensus sequences, the “stronger” the promoter,
meaning the more likely RNA polymerase binding
and transcription will occur.
Consensus sequence
Numbers indicate the
percentage of different genes
in which that nucleotide
appears in that spot in the
promoter sequence.
http://www.uark.edu/campus-resources/mivey/m4233/promoter.gif
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DNA regions- eukaryotes
Binding of factors to the TATA box area essential for
transcription to occur. Binding of factors to the promoter
influence how much transcription occurs.
http://web.indstate.edu/thcme/mwking/gene-regulation.html
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Promoter and protein factors
CAAT box
TATA box
Other promoter elements
such as hormone response
elements.
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What happens at the promoter
• TFIID: a multicomponent protein made of
– TBP: TATA Box Binding Protein
• Actually binds to the TATA box on DNA
– TAFs: TBP Associated Factors
• Ten to 14 proteins that bind to the TBP
– This complex , along with other TFs, recruits the
RNA pol II so it can begin transcription
• Unlike on prokaryotes, the RNA Pol II does not
actually bind to the TATA box of promoter.
See also cats.med.uvm.edu/.../ 2.1.grg.promoter.html
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What happens at promoter
Based on: http://www.nig.ac.jp/section/mitsuzawa/mitsuzawa_fig.jpg
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Enhancers
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• Short DNA segments that enhance transcription
– “silencers” apparently exert negative control
• Important aspects of enhancers
– Specificity: certain sequences bind to certain
transcription factors
– Can be located upstream, downstream, within the
gene, at a considerable distance from promoter.
– Can be inverted without changing affect.
– Promote looping of DNA, a 3D change that
somehow promotes transcription.
How enhancers work
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Specificity: Depending on why gene
is needed in the cell, a unique
enhancer sequence is bound to by
one transcription factor, but not
another.
Multiple enhancers: transcription can
be increased by several different
signals (transcription factors binding
to several enhancers).
http://www.emunix.emi
ch.edu/~rwinning/genet
ics/eureg3.htm
How enhancers work-2
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Enhancer promotes DNA looping which leads to
increased transcription. The “enhancer-binding protein”
shown would also be called a transcription factor in most
textbooks.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html#enhancers
More on Transcription Factors
• Proteins that bind to DNA
– Helix-turn-helix
– Zincfinger
– Leucine zipper and other
unique-named motifs
• TFs typically have more than 1
domain, also bind to other
proteins.
– Bind at core promoter, at
upstream promoter elements, or
at enhancers.
http://www.web-books.com/MoBio/Free/images/Ch4F5b.gif
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For more viewing
• www.bmb.psu.edu/.../
tan/lab/gallery_protdna.html
• 3D imaging of transcription
factor binding to DNA.
Leucine zipper
http://www.uic.edu/classes/bios/bios100/mike
/spring2003/leucinezipper.jpg
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Other controlling factors
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• Chromatin remodeling
– Chromatin remodeling complexes
• Specific proteins disrupt nucleosomes, make
DNA available to be transcribed
– Acetylation of histones
• Causes histones to bind DNA less tightly
– Methylation: nearly universal way of decreasing use
of DNA
• Methyl group blocks access of proteins
• Barr body, other un-transcribed DNA highly
methylated.
Two short examples
• Endocrine tissues send a chemical signal to a target
tissue, how does this effect gene expression?
• Steroid hormone
– Lipid substance, diffuses through cell membrane
– Binds to its receptor = a transcription factor.
– Enters nucleus, turns on appropriate genes.
• Binds to enhancers/promoter elements
• Peptide hormone
– Binds to receptor on cell surface
– Triggers 2nd messenger which activates a
transcription factor.
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Other methods of genetic control
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• DNA changes
– rearrangements (e.g. antibody genes)
– Methylation of C (many GC rich regions)
• At level of mRNA
– Differential splicing: different proteins.
– De-adenylate tail, decap: nuclease destroy mRNA.
• At the level of Translation
– mRNA can be sequestered, used later.
– Lot of mRNA means lots of translation, product
• Post-translational modification
– Phosphorylation, methylation, acetylation, etc.