Chromatin Remodelling And Repression Flashcards
What are the readers in the histone code
Bromodomains
Chromodomains phD
It’s proteins which read the post translational modifications
Other than acetylation Nd methylation. Which other way can chromatin be remodelled
Atp dependant chromatin remodelling
What type of ATPase do all atp dep remodelling complexes have
Snf 2
There are 4 subfamilies of the super family 2 atp dep remodelling complexes. What are they
Snf2/swi2
ISWI
Chd/mi2
Ino80
What characterises swi2/snf2 remodel complex
A bromodomain and a snf2 ATPase
What characterises chd/ mi2 remodeller
Chromodomain and a dna binding domain
And the snf 2 ATPase domain
What characterises the ino 80 complex
A split ATPase domain
What do remodellers like chd mi2 use ATPase hydrolysis for
Sliding, unwrapping, spacing, evicting nucleosomes
And
Histone variant exchanges
What does swi2/snf2 remodellers do using the snf2 ATPase
Induce torsions in dna and change the position of dna around nucleosome
What do atp remodelling complexes work with
Hats like tra1 which is bound to gcn5 activator
How is bromodomain of snf2 attracted to tra1 HAT
Because tra1 has acetylated lsyines around it and the bromodomain of snf2 recognises this
What does hat and atp complexes cooperation do
Allow pic recruitment
What genes does snf2 in yeast regulate
Genes at end of mitosis
What role does human snf2 have in cell cycle regulation
Interacts with cyclin E and Rb (tumour repressor) repressor
What would mutation in snf2 in humans cause
Tumours
Snf2 is used for tumour suppression
Snf2 is important for transcription factor expression. Give examples
HSF, myoD, glucocorticoid and retinoids receptors
Can atp dep remodelling also cause repression of txn
Yes
Which enzymes are important in repression
HDACs and histone methylases HKMT via lys 9 and 28
How do HDACs repress
Hypoacetylate lysine residues on n terminal tail via hydrolysis
Adds positive charge back to lysine
Dna will tightly bind to nucleosomes
Just like hats are co activators with snf2, what are HDACs
Co repressors
What are class 1,2 and 4 HDACs dependant on
Zinc
What is class 3 sir 2 HDACs dependant on
Nad
Which repressor gene that has a dna binding domain forms a complex with HDACs for co repression
Ume6 gene
Which complex is formed by the corepressors ume6 and rpd3 HDAC
Sin3
What genes do sin3 repress
Meiosis genes
Which atp dependant remodeller is a repressor
NuRD - mi2/chd family
How does nuRD repress
Decreases spacing of nucleosomes fotming CLOSED CHROMATIN
Does the nuRD repressor also have a HDAC
Yes
Histone lysine methyl transferases hkmt are repressing if at lys 9 and 28, is this found in heterochromatin
Yes
Aswell as hkmt at 9 and 28, what other properties does hetereochromatin have
Hypoacetylation via HDACs
And
Association with silencing factors
How is H3 lys 9me produced in heterochromstin
Lys 9 is deacetylated via HDACs
Then a hkmt methylated the lysine 9 (K9)
This is recognised by chromodomain proteins HP1 of tri and di methyl groups
HP1 will form compact nucleosomes and recruit other repressors
What is HP1
Heterochromatin protein 1 with a chromodomain
Which hkmt methylates H3 lysine 9
Suvar 39
Which reporter gene is used in a reporter silencing assay to analyse heterochromatin
Ade6, when expressed it turns white
What happens when ade6 is placed in heterochromstin region
Switched off and adenine intermediate turns red
Which non coding rna is switched on during development to inactivate an X
Xist
Which hkmt is attracted when xist is switched on for repression
H3k27 methylases
What does hkmt h3k27 do when recruited by xist to repress x
Recruit other silencing factors to inactivate the x
