L7, Epigenetics Flashcards
1
Q
Definitions of epigenetics: (Particularly molecular definition)
A
- Inheritance of any change in gene function that does not involve a change in DNA sequence
- Persists in absence of the initiating signal
- Molecular: Chemical modification of histones and DNA because these are required for or contribute to a heritable change in gene expression
2
Q
Reminder: Nucleosome structure
A
- 10nm diameter
- 8 core histone proteins with DNA wound around 2x
- Tails interact with other nucleosomes to compact DNA -> typical site for modification (K, R, S, P residues)
3
Q
Chromatin modifications: Effects and usefulness
A
- Affecting chromosome accessibility
- Inherited -> stable mitotically speaking but still reversible changes
- ncRNAs (e.g. Xist)
4
Q
Main types of epigenetic modification:
A
- Modifications of DNA
- Modification of histones
- Assembly of protein structures on DNA
5
Q
Properties of heterochromatin:
A
- Highly condensed; generlly not transcribed
- Typically low gene density
- Replicates late in S phase
- Often localised to nuclear periphery
- No meiotic recombination is possible in these regions
- Typically heavily methylated with characteristic PTMs of histones
- Either constitutive (all cells the same) or facultative (e.g. Inactive X)
6
Q
How is CpG methylation enacted? How may it be reversed?
A
- DNA modification
- De novo methylase adds methyl group to cytosine (does not affect base pairing) e.g. DNMT3a/b
- Perpetuation methylase add Me to hemi-methylated strand e.g. DNMT1
- Methyl group is removed by Demethylase enzymes
7
Q
What is the function of CpG islands?
A
- Typically found in promoter regions of mammalian genes
- Leads to constitutive expression as the action of DNTs meaning they tend not to get methylated
- Weaker, less dense CpG sequences can be regulated so can be either methylated or unmethylated
- This is a heritable change
8
Q
How is heterochromatin created after replication?
A
- Created by self-assembling complexes, part of which remain bound after replication
- This allows the bound proteins to recruit more subunits to daughter chromosomes
9
Q
Well-characterised sites on H3 tail for modification:
A
- Mono, di or tri methylation of H3K9 and H3K27
- K = Lysine
- H3K4 demarcates euchromatin
10
Q
What types of proteins regulate epigenetic marks?
Give example
A
- Writers (histone acetyl transferases, serine/threonine kinases, PRMT, HKMT)
- Readers (proteins with chromo- domains etc)
- Erasers (histone deacetylase, protein phosphatase , deiminase, amine oxidase hydroxylase)
11
Q
Readers for acetylation vs methylation:
A
- Acetylation recruits Bromo-domain containing proteins, facilitating euchromatin -> ACTIVE
- Methylation recruits chromo-domain containing proteins -> can vary but generally leads to heterochromatin -> transcriptional repression
12
Q
Example: Formation of heterochromatin
A
- Typically coupled events, often with positive feedback loops in action
- Eraser: HDAC removes Ac from H3K14
- Writer: Allows SUV39H1 to trimethylate H3K9
- Reader: HP1 binds H3K9me3 -> able to propagate condensing signal due to self aggregation
13
Q
Heterochromatin protein 1 (HP1): Key domains and interactions
A
- Chromodomain: binds to specific methylated lysines (K), often associated with transcriptional silencing
- Linker domain
- Chromoshadow domain: facilitates interaction with itself and other proteins -> thus able to self-aggregate, propagating condensing signal -> also interacts with DNMT1 and H3K9 methyltransferase (positive feedback loop)
14
Q
+ Further feedback loop examples (slide 20)
A
- Pericentric heterochromatin
- Repression via HDAC, Sin3A and MeCP2
- Further repression…
15
Q
+ How is the spread of heterochromatin limited?
A
Barrier regions -> physically halting positive feedback loops
- e.g. Nucleosome depletion
- e.g. Nucleosome turnover
- e.g. Opposing PTMs
- e.g. PTM-mediated eraser recruitment
