Gene-L4- Genome II Chromatin Remodelling

what is chromatin remodelling and why is it necessary for DNA function?

• chromatin remodelling- physically wrestling chromatin to change DNA accesibility

• involves enzymes that can modify histones and chromatin structure

• needed: to control accessibility of DNA to regulatory proteins for DNA replication, DNA repair, gene expression. changes how highly DNA is packaged around histones

what are chromatin remodelling complexes and how do they use ATP?

• chromatin remodelling complexes are large multi protein complexes

• they use ATP to temporarily change the nucleosome structure

• ATP is needed as DNA is neg and histones are pos- strong binding and needs to be overcome

• targets H2A and H2B dimers- more looser

• remodelling complexes: sliding nucleosomes along DNA and increase accessibility and repositioning histone cores

what is the process of chromatin remodelling complex? describe the 2 step process and what this allows?

• cyclic 2 step process

1. disrupt nucleosome structure by using ATP to increase accessibility

2. reassemble nucleosome after access

• this allows the transition between euchromatin and heterochromatin

what are the effects of chromatin remodelling?

• nucleosome sliding- nucleosomes move along the DNA sequence and needs ATP

• spacing between nucleosomes can be looser or tighter

• nucleosomes can be removed from DNA

what is the role of histone chaperones in chromatin remodelling and replication? why’s it needed in replication?

• histone chaperoneL: proteins that bind histones and nucleosomes

• they transport nucleosomes to new DNA locations

• or they can remove histones from DNA and put them elsewhere

in replication- DNA is duplicated and nucleosome number must also be doubled, ensures the correct reassembly of chromatin after replication. maintains genetic organisation

what happens to nucleosomes during DNA replication?

• replication machinery must displace histone octamers to allow DNA synthesis

• parental nuc,eosomes are redistributed onto daughter strands

• nucleosomes are temporarily dismantled and reassembled behind the replication form

• chromatin structure is disrupted and rapidly restored

how are nucleosomes reassembled during DNA replication and what does CAF-1 do? what do new chromatin contain?

• histone chaperones like CAF-1 guide nucleosome reassembly

• CAF-1 transfers histones from a parental nucleosome onto daughter DNA strands

• newly formed chromatin has: old parental histones and newly synthesised histones

• makes hybrid nucleosomes

how is histone production co-ordinated during S phase?

• histone production is tightly linked to the S phase- DNA synthesis phase

• histone genes are highly transcribed during S phase- 50 fold increase

• multiple histone gene copies- allow rapid simultaneous transcription- H2A genes

• also histone mRNA is unstable and rapidly degraded after translation and so this prevents excess histone accumulation

how does covalent histone modification regulate chromatin structure and DNA accessibility

• chromatin structure is regulated by chemical modifications of histone tails

• N terminal have lysine and arginine residues and regulate with negatively charged DNA

• outcome determines if its euchomratin or heterochromatin

main types of histone modifications- 4

• acetylation of lysine from pos to neutral→reduces histone DNA affinity- opens it

• methylation of lysine→keeps it positive but makes 3d binding surfaces

• methylation of arginine→monoid,tri and maintains pos charge

• phosphoprytlation of serine→ adds neg charges

what are the main histone modifying enzymes and how do they regulate chromatin accessibility? 5

1. histone acetyltransferases HATs- adds acetyl groups to lysine residues to increase accessibility and allow more transcription

2. histone deacetylases- HDACs- removes acetylene groups and decrease accessibility for heterochromatin and gene silencing

3. histone methytransferases- adds methyl groups

4. kinases- adds phosphate groups to serine

5. ubiquitin transferases

what is the histone code and how does it regulate gene expression? how are they identified ?

• histone code is the pattern of histone modifications that determine chromatin state and gene activity

• read using antibodies or protein specific for modification

what are the key histone code markers?

• H3K9me3- lysine 9-gene silencing

• H3K27me3- gene silencing- recruits polycomb repressive complexes for chromatin compaction

• H3K4me3 + H3 acetylation- active transcription

how is the histone code interpreted by writers, erasers and readers?

1. writers- enzymes that add modifications. HATs acetyltransferases and methyltransferases

2. erasers- enzymes that remove modifications. histone deacetylaces

3. readers- proteins that recognise modifications and recruit downstream complexes. bind modified histones and trigger responses. can recruit additional readers to amplify of chromatin states by spreading silencing or activation

how does acetylation of histones regulate transcription

• regulated by balance of acetyltransferases and deacetylation

• acetylation- neutralises the lysine positive charge and weakens DNA binding to open chromatin

• leads to inreased accessibility for TF and increased RNA polymerase recruitment for active transcription

• deacetylation- compacts chromatin and represses transcription

discuss activators and repressors? what they do and what is in them?

1. transcriptional activators

• multiprotein complex

• Regulator A has acetyltransferase activity or interact with HAT complexes for hyperacetylation- allows binding and promotor to TF

2. transcriptional repressors

• multiprotein complex

• interact with HDACs to deacetylate lysine