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.

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.

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.html

8. What happens at promoter
Based on:

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).

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.

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.

13. For more viewing www.bmb.psu.edu/.../ tan/lab/gallery_protdna.html
3D imaging of transcription factor binding to DNA.
Leucine zipper

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.

15. 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.

16. 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.