L15: Regulation of transcription II Flashcards
1
Q
Sequences for regulation of transcription found distal to start site
A
- Enhancer sequences
- Often contain high density of sites for binding of regulatory proteins
- Either upstream or downstream of the gene
2
Q
Histone acetylation
A
- Hypoacetylation: Strong inter-nucleosomal interactions; histone tails constrain wrapping of DNA on nucleosome surface (HDACs)
- Hyperacetylation: Weak inter-nucleosomal interactions: hsitone tails do not constrain DNA, accessible to TFs (HATs)
-> acetyl grps can also directly recruit proteins via bromodomain proteins
3
Q
Chromatin remodelling complexes
A
- e.g. SWI/SNF
- Use ATP to move the histone octamer
- They can be recruited either sequence-specifically or by histone modification
4
Q
Conditions associated w/ changes in methylation pattern
A
- Fragile X syndrome
- Cancer
- During ageing
5
Q
Interaction between DNA methylation and histone modification
A
- Methyl groups on either DNA or histone tails can recruit methyl-binding proteins which serve to recruit other proteins that modify chromatin
-> affects gene expression - Various other interactions occur
-> very complex interactions
6
Q
DNA methylation and transcriptional control
A
- Methlyation affects chromatin structure and transcription
- In the DNA of some euks, cytosine residues are methylated at CpG sites
-> transcriptionally active genes - lower levels of DNA methylation
7
Q
The mediator complex
A
- As well as general transcription factors, RNA pol II requires the Mediator Complex
- Consists of approx. 20 proteins and is 1 MDa in size
8
Q
ELK1 ( in absence vs presence of mitogens)
A
- In the absence of mitogens, ELK1 binds to serum response factor (SRF) but doesn’t activate transcription
- Mitogen-activated signal transduction pathways phosphorylate ELK1
- pELK1 recruits mediator, promoting transcription
-> expression of proliferative genes
9
Q
GAL genes in yeast (overview)
A
- GAL1, GAL7, GAL10 encode enzymes that function in a pathway to metabolise galactose (whilst this is analogous to the lac operon, operons are almost never found in eukaryotes)
- W/out galactose, no transcription, similarly when glucose is available (exerts catabolite repression)
- Galactose available, glucose not available: rapid transcription
- GAL4: regulatory protein binds to UASG (upstream activator sequence-galactose)
10
Q
Inducible transcription process in GAL genes
A
- Gal4 activates transcription by binding to UASG sequence
- In absence of galactose, Gal80 binds to Gal4, preventing transcription
- When galactose present, Gal3 binds to Gal80, preventing Gal80 binding to Gal4
-> Ga4 recruits SAGA and Mediator (activates transcription)
11
Q
Nuclear receptor proteins
A
- Bind to particular signalling molecules (>50 in humans) e.g. oestrogen receptor
- Ligand binding leads to a conformational change that allows them to drive transcription
- in some cases binding to the ligand allows translocation to the nucleus e.g. the glucocorticoid receptor
-> 2 levels (whether they interact w/ corepressor etc. and where in cell they are)
12
Q
Transcriptional repression in nutrient sensing in yeast
A
- W/ sufficient N, C source; Ume6 binds DNA and recruits co-repressors (Sin3, Rpd3, Isw2)
- Rpd3: Histone deacetylase
- Isw2: nucleosome remodelling enzyme
- W/out sufficient , C; Ume6 phosphorylated, Sin3 and Rpd3 dissociate, Ime1 (co-activator) recruited
13
Q
Promoter proximal stalling
A
- Promoted by negative elongation factors (e.g. NELF, DSIF)
- Occurs after RNA pol II has transcribed 35-50 bps
- Relief of this pausing allows transcriptional elongation to proceed (RAPID response to change)
e.g. expression of gene that encodes Drosophila Hsp70 protein (chaperone that protects cells from high temperatures)
14
Q
hsp70 transcription (w/ vs w/out heat shock)
A
- w/out heat shock, GAGA TFs bind and recruit NURF (nucleosome remodelling factor) -> exposes control elements (TATA, HSE). However, negative elongation factors (NELF, DSIF) prevent phosph. of Rpb1 C-term domain
- w/ heat shock: temperature rise causes Hsf to form a trimer, which binds to HSE sequence, and interacts w/ Mediator to recruit a kinase and CTD is then phosph., relieving pausing