Control of eukaryotic gene expression

1
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

2
Overview of critical elements

• 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)

3
The Process of Transcription

• 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.

4
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/p
romoter.gif
5
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-regulati
on.html
6
Promoter and protein factors
TATA box
CAAT box
Other promoter elements such as hormone response
elements.
7
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.ht
ml
8
What happens at promoter
Based on http//www.nig.ac.jp/section/mitsuzawa/m
itsuzawa_fig.jpg
9
Enhancers

• 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.

10
How enhancers work
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.emich.edu/rwinning/genetics/eur
eg3.htm
11
How enhancers work-2
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/BiologyP
ages/P/Promoter.htmlenhancers
12
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/sprin
g2003/leucinezipper.jpg
14
Other controlling factors

• 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.

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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

• 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.