Week 3 Chromatin/Epigenetics Flashcards
what structural motif allows specific histone interactions
- Globular domain contains a histone fold motif that provides the basis for dimerization interface– handshake interaction
describe structure/components of nucleosome
smallest repeating unit of chromatin
- 147 bp DNA wrapped around an octamer of histones
4 distinct histones– 2 of each type
briefly explain the use of MNase sequencing in mapping chromatin structure
what is the end goal (think occupancy)
- exo/endonucleases used to digest naked DNA betw/ Nucleosomes
– remaining undigested DNA subjected to high throughput seq.— mapped on reference
gives idea of nucleosome occupancy on DNA
in what do transcriptional activators (which bind to enhancer cis-regulators sequences) facilitate the altering of local chromatin structure?
- T activators attract coactivators ATP-dep chromatin remodellers, histone-mod enzymes, histone chaperones
how do transcriptional activators bound to enhancers 1000s of KB away from promoter facilitate assembly?
- bonus: what is the role of mediator complex in this?
DNA looping– brings T activator into close proximity to promoter
— mediated by MEDIATOR protein—ties interaction between T activators, RNAP, GTFs and their assembly at promoter
how does histone chaperone mediated replacement and removal of histone affect DNA access?
REMOVAL– allows assembly of transcription machinery on histone free DNA
REPLACEMENT —shifts chromatin structure so there is greater access to nucleosome DNA
How does DNA methylation repress transcription/ promote heterochromatin formation
- methylated DNA acts as binding site for histone modifying enzymes– induce heterochromatin conformation
Xist (along with Tsix) is produced from XIC cis-acting region of X chromosome.
give examples of 1ry/2ry silencing factors induced by Xist and how they induce changes in chromatin structure (i.e. lead to X chromosome compaction)
1ry
Depletion of acetylation, H3K4me (at enhancer site)
- accumulation of H3K27me (facultative heterochromatin)
2ry
DNA methylation of genes promoters– H3k4me3
when are chromatin structures disassembled in cell cycle
S phase
what enzyme facilitates maintenance methylation i.e. methylation of hemi-methylated DNA strands (right after daughter strand synthesis)
- what accessory protein needed in vivo?
what process is DNA methylation coupled to (hint: H3K9me3)?
- maintenance methylation facilitated by DNMT1— preference for hemi-methylated DNA where one strand has unmethylated CpG site
- maintenance methylation in vivo requires UHRF1 protein
coupled to Histone methylation via Suv39 writer which methylates K9 on H3
outline the positive feedback mechanism between HP1 (reader) and Suv39H1 and the outcome
HP1 reader recruits Suv39 and facilitates methylation of neighboring chromatin at H3K9 sites– induces repressive chromatin form
– way by which heterochromatin is established
distinguish between direct histone modifications acetylation and methylation
acetylation– reduces histone positive charge—disrupts electrostat. Histone-DNA interaction– less compact chromatin—DNA ACCESS
methylation– promotes positive histone charge– leads to more compact chromatin
describe the result of histone chaperone-mediated replacement of H2A histone with H2A.Z on chromatin structure and overall gene transcription
- think of nucl. barrier, elongation
dimers including H2A.Z are more easily lost during nucleosome unwrapping (which occurs ahead of repl. fork) — LOWER NUCLEOSOME BARRIER
—that DNA becomes accessible— RNAPII elongation
how do the following chromatin remodeling complexes affect chromatin access?
- SWI/SNF
- ISWI/CHD
- INO80
SWI/SNF- facilitates chromatin repositioning– nucleosome ejection/dimer eviction
INO80–facilitates histone exchange
ISWI/CHD– nucl. maturation/spacing
what modifications do the following domains recognize?
- Bromo domain
- Sant domain
- chromo domain
- acetylation on K
- phosphorylation of K, T residues
- methylation of K
