Transcription factors and Enhancers

Question 1

Describe the characteristics of Transcription factors and the enhancer + promoter

Answer 1

1. Transcription factor: trans-acting factor that can influence transcription
2. enhancer + promoter is cis-acting region that can influence transcription

• enhancer is 72 bp repeats and the promoter has GC boxes + TATAA box

Question 2

The transcription factors/activators

Answer 2

1. Basal TF: factors required for all promoters (ex) TBP
2. Upstream factors: ubiquitous, constitutively present
3. Inducible factors: environmental conditions, cell-type specific protein

• DNA-binding domain
• Activation domain
• mediator

Transcription activators contain a DNA-binding domain and and an activation domain (protein-protein interactions).

They can compete with repressors for the
Same DNA sequence.

Question 3

Families of DNA-Binding Domains-the most common

Answer 3

1. Zinc Fingers (zinc ion, alpha helix, beta sheet)
2. Helix-turn-Helix
3. Leucine Zipper (dimers)
4. Helix-loop-Helix
5. Helix-wing-Helix

Binding can be either to major or minor groove of the dsDNA

Sequence specificity

Question 4

How do we find transcription factors?

Answer 4

1. Isolate nucleus of cell
2. lyse, isolate nuclear proteins
3. determine which proteins bind promoter sequences

what are transcription factors? How do we find them?

Need to isolate DNA (chromatin) form the cells

Gent nuclei, lyse them and isolate the nuclear proteins

Use the extract in combination with a piece of DNA of known sequence and test for occupancy of specific sites

Question 5

What is the action of transcriptional Acitivators?

Answer 5

1. Transcriptional activators can interact directly with mediators or general transcription factors.
2. They can also influence chromatin structure through interactions
3. With histones or chromatin-associated proteins.
4. They often recognized specifically post-translationally modified histones.
5. Usually requires a co-activator

Question 6

Action of transcriptional Repressors

Answer 6

1. Direct competition for DNA-binding site or through occupancy of the mediator/activator interface. The repressor competes for DNA binding
2. Chromatin structure and composition can also be modified
3. By the recruitment of co-repressors (often recognizing modified histones)

Co-repressors can also affect chromatin structure and composition

Question 7

Regulation of transcritional elongation Part I

Answer 7

1. Preinitiation complex
2. Phosphorylation of CTD serine-5
3. Initiation of transcription
4. TF II H phosphorylates Ser-5
5. CTD: C-terminal domain of RNA Pol II

Question 8

Regulation of transcriptional elongation Part 2

Answer 8

1. Paused polymerase
2. Recruitment of negative regulators cases pausing
3. NELF and DSIF are negative regulatory factors
4. CTD and processing factors
5. Release of negative regulators
6. phosphorylation of NELF, DSIF, and CTD serine-2 by P-TEFb

Question 9

Regulation of transcriptional elongation Part 3

Answer 9

1. productive elongation
2. additional elongation and processing factors
3. end of promoter clearance recruitment of elongation factors and processing factors