Lecture 15 Flashcards
What sequences allow for regulation of transcription?
Enhancer and silencer sequences
Contain high density of protein sites for regulatory protein binding
Describe eukaryotic regulatory proteins
Recognise specific DNA sequences
Modular
Additional domains aid oligomerization, repress or activate transcription, interact with regulators
Why do regulatory proteins recruit other proteins?
Other proteins help regulate transcription
Do not have DNA-binding activity themselves
Modification at lysine residues by histone acetylation
Hypoacetylation - Strong internucleosomal interactions: Histone tails constrain wrapping of DNA on nucleosome surface
Hyperacetylation - removes positive charge from lysine chains - Weak internucleosomal interactions: Histone tails do not constrain DNA, which is accessible to transcription factors
What do bromodomain proteins do?
Allows acetyl groups to directly recruit proteins
What carry out acetylation and deacetylation?
Histone acetyl transferase (HATs)
Histone deacetylases (HDACs)
Why are binding sites for transcription factors inaccessible?
Binding sites for transcription factors can be inaccessible as DNA wrapped around nucleosomes
What do chromatin remodelling complexes do?
Use ATP to move histone octamer - recruited sequence specifically, or by histone modification
Explain DNA methylation
Affects chromatin structure and transcription
- Cytosine at CpG sites methylated in eukaryotes
What lowers DNA methylation?
Transcriptionally active genes
What is transcriptional silencing
Hypermethylation
What factors contribute to changed methylation pattern?
- Fragile X syndrome
- Cancer
- Aging
What enzyme converts cytosine to 5-methylcytosine
DNA methyltransferase
How can methylation affect gene expression
Methyl group recruit methyl-binding proteins
Recruit proteins that modify chromatin
Other than transcription factors, what does RNA polymerase II require to bind the promoter?
Mediator complex
Mediator complex structure
20 proteins and 1MDa in size
ELK1 recruitment of mediator complex in proliferation
ELK1 binds serum response factor, but doesn’t activate transcription in absence of mitogens
Mitogen-activated signal transduction pathways phosphorylate ELK1
Phosphorylated protein recruits mediator, promoting transcription
Proliferative genes expressed
Activation of GAL genes in yeast
- GAL1, GAL7, and GAL10 encode enzymes that allow galactose metabolism
- Not an operon
- Absence of galactose - No transcription
- Glucose present: No transcription - glucose exerts catabolite repression
GAL4 - Regulatory proteins binds UASG
What does Gal4 do?
Binds UASG sequence
Gal80 binds Gal4 in galactose absence - no transcription
Gal3 binds Gal80 in galactose presence - prevents Gal80 binding Gal4 - Gal4 recruits SAGA and mediator - Activates transcription
transcriptional repression in nutrient sensing in yeast
- Ume6 responds to nutritional cues
- Activates or represses transcription
- Another N and C causes Ume6 to bind DNA - recruits Sin3, Rpd3, Isw2
Rpd3 is a histone deacetylase
Isw2 a nucleosome remodelling enzyme
What occurs if Nitrogen and Carbon absent in nutrient sensing
Sin3 and Rpd3 disassociate
Co-activator Ime1 recruited
When does RNA pol II often stall
After 35-50bp
Promoter proximal stalling by NELF and DSIF
What are NELF and DSIF
Negative elongation factors
hsp70 transcription
GAGA transcription factor binds and recruits NURF in absence of heat stress
NURF alters chromatin structure - exposes chemical control elements
NELF and DSIF prevent phosphorylation of Rpb1 C terminal domain
Hsf protein form trimer if temp rises
Trimer binds HSE sequence
Interacts with mediator - recruits kinase, CTD phosphorylated, pausing relieved
