BIOC2306 Histone Code

what is pluripotency

the ability to differentiate into any type of cell

do repressive epigenetic marks cooperate with eachother (DNA methylation and histone mods)

Yes

Histone Code hypothesis

modifications of histone tails determine which proteins are bound and whether an active or repressive chromatin structure is generated

3 types of proteins in epigenetics

writers, readers and erasers

how are there nearly 80 core histone modifications possible

diff mods at diff sites

can anything beyond the core histone octamer be modified

yes, mod H1 (linker histone) and its variants

what enzymes catalyse acetylation of histones

HATs Histone acetyltransferases

what molecule supplies the acetyl group for histone mods

Acetyl CoA

which residue in histone tails can be acetylated

lysine

how does histone tail acetylation result in a more open chromatin structure

acetylation neutrilises the negative charge of lysine on histone tails, weaking their interaction with DNA in adjacent histones

prev 30 nm fibre formation

what technique can be used to show histone acetylation is associated with more open chromatin structure

gradient sedimentation/differential centrifugation

acetylated more open, transfer distance less

what proteins bind acetylation marks

proteins with bromodomains

(readers)

what proteins have bromodomains

HATs and histone remodelling complexes

what part of DNA is acetylated by HATs (coactivators)

active promoters

role of deacetylases (HDAC)

remove acetylation modification

fast acting

why are acetylation marks on histones not ‘epigenetic’

v dynamic marks, therefore often turnover of marks (by HDACs and HATs) before inherit

how can lysine be methylated

mono di or trimethylated

is histone tail methylation an active or repressive mark

can be active or repressive mark

which histone is often methylated

histone H3

which H3 methylations can occur

4, 9, 27, 36

which nucleosomes often have H3K4me3

first 5 nucleosomes of/near the promoter

which enzyme mediates H3K3me3 modification near the promoter

Set1

how does Set1 associate with RNA pol II

associates with pi form of Ser5 of CTD (C terminal domain)

what proteins are H3K4me3 a binding site for

proteins with Plant homeodomain (PHD) finger

(transc activators)

what part of DNA is the H3K4me1 mark associated with

active enhancers

what part of DNA is the H3K4me3 mark associated with

actively transcribed genes

how does Set2 assocaite with RNA pol II

with the pi form of Ser2 of the CTD

role of Set2 associated with RNA pol II

methylates nucleosomes in the transc region of genes (not promoter)

form H3K36me3 mark

resetting of transcribed chromatin

what mark does Set2 make

H3K36me3

resetting of transcribed chromatin process

for transc req eviction of H2A/2B dimers

HATs assoc with pol II acetylate nucleosomes to help displace them for transc

after transc H3K36me3 recruits HDACs to remove acetylation (retset) favouring recruitment of H2A/2B dimers

how does the H3K36me3 mark help prevent unwanted transc of rep DNA

recruits HDACs to remove acetylation that HATs add (to help gen open chromain for rep) promoting recruitment of H2A/2B dimers, form closed form

are H3K9me3 and H3K27me3 active or repressive marks

repressive

protein interactions involved in heterochromatin formation favour what

the spreading of heterochromatin

how do proteins inv in Heterochromatin formation favour the spreading of HC

reader-writer complexes bind H3K9me3 and H3K27me3 marks and catalyse their formation on adjacent nucleosomes

what protein domain binds H3K9me3

HP1 (heterochromatin protein)

via chromodomain

what do bromo and chromodomains bind

acetylated K

methylated K respectively

how does HP1 bind H3K9me3 marks

via its chromodomain

which enzyme methylates H3 at K9

Suv39h via its SET domain

what domain is involved in the acetylation of histones

SET domain

role of Suv39h

methylate H3 at K9

(histone methyltransferase)

what enzyme does HP1 recruit

Suv39h

how does HP1 binding promote other HP1 mols binding

HP1 binds H3K9me3 via chromodomain

recruits Suv39h

cat formation of H3K9me3 mark (via SET domain) on adjacent nucleosomes

HP1 can bind new mark therefore spreads

what is position effect variegation

differential spread of heterochromatin in drosophilia eye cells cause silencing of eye colour genes in some cells (become white, not red) get mix in eye colour

inherit gene silencing

what stops the spread/propagation of heterochromatin

insulator elements

what mark do polycomb group proteins associate with

H3K27me3

role of polycomb group proteins

maintain gene repression

(dont establish it)

how are genes silenced early on in development and continue to be silenced

proteins bind gene to be repressed and establish repression

recruit polycomb group proteins

repressor can be lost but PcGs remain so stays repressed

what are PRCI and PRCII

polycomb repressive complexes I and II

role of PRC I

bind H3K27me3 mark via chromodomain

role of PRC II

methylates H3K27 via SET domain

if PRCs I and II require H3K27me3 marks to bind to catalyse their formation, how is the mark first established

recruitment proteins bind PRE (polycomb repressive element) in DNA that recruit PcGs

role of PRC I and II together

facilitate spreading of heterochromatin

what is the majority of heterochromatin bound by (70%)

HP1 and/or PcG protein bound

is H3K14Ac repressive or active mark

active (bound by bromodomain proteins)

how are chromatin modifications maintained after replication

H3H4 tetramer from parental DNA maintained after rep fork

CAF1 deposits newly synth H3H4 tetramers to fill gaps on daughter strands (using Asf1 H3H4 cochaperone)

old histones prov template to recruit modifying enzymes and reestablish the histone modifications within a chromatin domain (1/2 daughter nucleosomes have mod)

(reader writer complexes recognit same mods they catalyse formation of)