BN - Transcriptional Regulation in Eukaryotes Flashcards
What is the role of transcription factors (3)?
- Determine whether transcription occurs
- Determine cell specificity
- Confer response to specific timed stimuli
Why is determining the initiation mechanisms of transcription factors challenging?
Initiating transcription is challenging to determine due to low expression levels of transcription factors in cells
How do we identify transcription factors? (3)
- Bioinformatics analysis of whole genome sequencing data can identify regions up/downsteam of genes containing conserved sequences.
- Before that, mutation analysis (observational or interventional) of upstream regions to see what controls transcription
- Eventually identify multiple conserved sequences which appear to regulate transcription in different genes
What are the components of transcription factor structure?
TFs are proteins made up of amino acids hence their 3D structure is important to their function
Modular structure:
- One region binds DNA
- Another region binds to other components
What are the types of DNA binding domains in transcription factors?
- Zinc fingers
- Helix turn helix
- Basic binding domains
What are components of Zinc Finger Domains (6)?
- Contains a loop of 23 aa
- Usually have multiple zinc fingers per TF
- The linker between the fingers is 7-8 aa
- a-helix contacts the major groove of DNA
Often multiple zinc fingers are involved in binding the specific DNA sequence
Zn2+ ion does not directly interact with the DNA but is essential for the folding of the finger
Zinc fingers bind both to the major and minor grooves
What are some components of Helix turn Helix? (4)
- Two helices held at a fixed angle
- Recognition helix binds major groove of DNA
- Bind DNA as dimers, so the 2 recognition helices are separated by one turn of the DNA helix
Found in homeodomains
What are some features of basic (+ve charged) binding domains? (2)
- Transcription factors with basic binding domains cannot bind to DNA alone
- Transcription factors with basic binding domains must dimerise
What may TF activity be regulated by if responsiveness is important?
Location
e.g Steroid hormone receptors - Cys2-Cys2 zinc fingers
- Steroid hormones are synthesised in response to a variety of neuroendocrine activities
- They exert major effects on cell growth, tissue development and body homeostasis
What are activation domains?
A region of the transcription factor protein involved in activating/inhibiting transcription
What occurred in the domain swap experiment (4)?
- Combine DNA-binding domain of factor 1 with different regions of factor 2
- Test on a gene carrying the binding site for factor 1
- B-domain produces response
- Therefore domain B has activation domain of Factor 2
How do TF activation domains work?
Pre- initiation complex (PIC) is assembled
What are 2 key ways transcription activation factors can work?
a) Through direct interaction with the PIC
b) Through the recruitment of co-activators
- Work by interacting with the PIC
- Or by opening/loosening chromatin structure
Why do TFs recruit co-activators?
TFs recruit co-activators to modify histones
Histones: H2a, H2b, H3 and H4
-vely charged DNA wrapped around the +vely charged histones
How to co-activators alter chromatin structure? (3)
1. Histone acetyltransferase (HAT)
- Acetylates N-terminal tail lysine of histone units
- Neutralizes +ve charge of histone
2. Opens up DNA
3. Allows transcription factors & RNA polymerase II to get to the DNA
