Chromatin remodelling and transcriptional repression Flashcards
what enzymes are responsible for ‘Writing’ in the histone code
- Histone acetyl transferases
- Histone methyl transferases
- Kinases
what enzymes are responsible for ‘Erasing’ in the histone code
- Histone deacetylases
- Demethylases
- Phosphatases
what enzymes are responsible for ‘Reading’ in the histone code
- Bromodomain proteins
- Chromodomain proteins
- PWWP proteins
- PhD
Cells have multiple remodelling complexes, all have what?
Snf2-related ATPase
name all 4 members of the SWI2/SNF2 ATPase Superfamily
- SWI2/SNF2 superfamily
- ISWI subfamily
- CHD/Mi2 Subfamily
- Ino80 subfamily
how are the 4 distint subfamily characterised
additional domains and architecture of the ATPase domain
What additional domain does SWI2/SNF2 have
Bromo
What additional domain does ISWI have
SANT
What additional domain does CHD/Mi2 have
Chromo + DNA binding
How is Ino80 subfamily characterised ?
it has two ATPase domain and no additional domain
ATP-dependent Chromatin remodelling causes _
Sliding, unwrapping, eviction, spacing & histone variant exchange
what is the catalytic subunit of SWI/SNF
Snf2 (or Swi2)
in the presence of DNA or nucleosome, SWI/SNF hydrolyses _ ATP molecules per minute
1000
what other enzyme is Snf2 related two
DNA helicases
what is the hypothesised mechanism for Snf2
Thought to be a molecular motor that that uses the energy from ATP hydrolysis to track along DNA and induce torsion
how does Snf2 affect chromatin
disrupts histone-DNA interaction and movement of the nucleosome
which two enzymes regulate the same genes in yeast
SWI/SNF and the GCN5 HAT
HATs and ATP-dependent remodellers are commonly recruited to the same _
promoters
what is Snf2 help tether it to acetylated nucleosomes
Bromodomains
H_ & A_ function co-operatively
HATs & ATP-dependent remodellers
Yeast SWI/SNF regulates _ in genral transcripton and _ in cell cycle
- regulates expression of 5% of 6000 Y genes
- Regulates 25% of genes expressed at the end of mitosis
In terms of general transcription, Human SWI/SNF needs a number of what
transcriptional factors -glucocorticoid and retinoid receptor, heat shock factor and MyoD
what role does Human SWI/SNF play in the cell cycle
control the cycle via interaction with Rb & cyclin E
what role does Human SWI/SNF play in the development
deletion results in embryonic lethality
what role does Human SWI/SNF play in the tumour suppresion
mutations are associated with a variety of
tumour types
what are the chromatin modifying factors involved in transcriptional repression
- Histone Deacetylases (HDACs)
- ATP-dependent Remodellers
- Histone Methylases (heterochromatin)
where active regions of the genome are hyperacetylated, repressed regions are
hypoacetylated
HDACs function as _
co-repressors
How many major groups of HDACs are there
4
What are the groups which contain classical HDACs and what are they dependent on
Class I,II,IV
Zinc
how does Class III of HDACs differ from the others
Sir2 family, they require NAD as a co-factor
give an example of of a HDAC Co-Repressor Complexes which is conserved in yeast and mammals
SIN3 Co-Repressor
give an example of an ATP-dependent remodellers which commonly mediate transcriptional repression
The NuRD complex which belong to the Mi2/CHD family
what are the two basic types of chromatin
Euchromatin & Heterochromatin
describes Euchromatin
gene rich and with the potential to be transcribed
describes heterochromatin
gene poor, repetitive regions, transcriptional silencing
what are the biochemical features of heterochromatin
1) Hypoacetylation
2) Specific Histone H3 methylation (e.g. Lys9 & Lys27
3) Association of specific silencing factors
Heterochromatin Protein 1 is a _ protein
Chromodomain
Chromodomains often recognise and bind to which residue
methylated lysine
The chromodomain of HP1 is specific for _
H3 Lys9me2/3
Binding of HP1 is though to _
compact nucleosomal array and act as platform for the recruitment of further activities that prevent recruitment/activity of RNA pol II
What can be used to analyse heterohromatin
reporter silencing assay using fisson yeast
describe the experiment used for analysis of heterochromatin
Normal wild type - ade6 gene expressed white colonies
Silencing reporter strain - ade6 silence express red colonies (result from build up of a red pigment which is an adenine biosynthetic intermediate
A mutation in gene encoding a component of heterochromatin can caused what colour colonies in Heterochromatin Analysis
White/pink as ade6 silencing alleviated
what is X-chromosome inactivation
Female have 2 X chromosome, one of which is inactivated, this equalises the number of X-linked genes expressed in males and females
what is the condensed structure that is seen in the nucleus of inactivated X-chrm
Barr Body (assembled into a specific form of heterochromatin)
How does Inactive X (Xi) form
- Xist is inactive by Tsix during early development
-later in development Xist is upregulated which inactive Tsix - Xist coats chromosome and recruits H3K27 methylase, it goes on to recruit further silencing factors
what is the difference between inactive X (Xi) and active X (Xa)
Xa doesn’t have Xist unregulated and there for isn’t covered and doesn’t recruit silencing factors during late development
