MCB Lecture 27 Epigenetic Modifications Flashcards
… play a major role in stem cell differentiation
Epigenetic modifications
What are the functions of epigenetic modifications?
- Delineate the chromosome
- Package the chromosome
- Alter gene expression
What is the definition of an epigenetic modification? (3)
- Mitotic ally heritable
- Change in gene expression without change to DNA sequence
- Reprogrammed in gametogenesis
How does epigenetic modification have a role in chromosome structure?
Heterochromatin and euchromatic have different epigenetic modifications
What are the two forms of DNA packaging?
Differentiate between the two in terms of gene expression
Heterochromatin: dense, genes off
Euchromatin: loose, genes on
Describe the structure of a nucleosome
Octamer core of eight subunits (2x H2A H2B H3 H4)
H1 clamp
Histone tails protruding
How do histones form bonds with DNA?
Histones have a positive charge due to lysine and arginine.
The DNA is negative
Electrostatic interaction
What are the two categories of epigenetic modification?
DNA methylation
Histone tail modification
Describe the effect of DNA methylation
Genes are switched off
What does it mean when a gene is unmethylated?
Doesn’t necessarily mean that the gene is switched on
How is DNA methylation layed down?
De novo methyl transferases
Differentiate between the function of
DNMT1
DNMT3A
DNMT3B
DNMT1: maintains methylation after DNA replication
DNMT3A and DNMT3B: lay down methylation
Describe what happens to DNA methylation at DNA replication
One strand of the new double helix will have the original methylation
DNMT1 lays down methylation of the complimentary strand
When is DNA methylation layed down?
In early development
Describe the features of ICF syndrome
Immunodeficiency Chromosomal and Facial abnormalities
There is a mutation in the gene for DNMT3B
Thus, methylation is not layed down
Hypo methylation
How does ICF syndrome arise?
Mutation in the gene for DNMT3B
In ICF there is hypomethylation of … (4)
- Immune genes
- The inactive X chromosome
- Centromere
- Patterning
What are histone tail modifications?
The histone tails that protrude from nucleosomes undergo epigenetic modification
Which molecules lay down histone tail modifications?
What else can these molecules do to chromatin?
- Histone Methyltransferases
HMTs - Chromatin proteins
They remove or modify the modifications
What are the two types of histone modification?
Acetylation
Methylation
Describe the effect of acetylation on histone tails
Activation of the gene
What is the histone code?
Since where are many histone tails and there are many different modifications, the histone code is the overall effect of the histone tail modifications
How does histone acetylation work?
Acetylation of the tail leads to a decrease in the positive charge of the histone. It thus has reduced affinity for the DNA
What is the function of histone methylation?
Either activation or inhibition
What are the two histone methylations that result in inactivity?
H3K9me
H3K27me
What is the histone methylation that results in increased activity?
H3K4me
Differentiate between H3K9me and H3K27me
H3K9me : constitutive
H3K27me : facultative
How do the histone tail modifications affect chromatin packing?
The modifications act as a docking site for other chromatin proteins
These other proteins recruit factors that alter the structure of chromatin
What are some proteins that read histone tail modifications and bring about changes in chromatin structure?
CHD1
HP1
CBX2
How does CHD1 work?
What is it?
It unpacks chromatin
It is a chromatin protein
What does HP1 do?
What is it?
It recruits DNMT1
It is a chromatin protein
What does CBX2 do?
What is it?
It brings about other epigenetic modifications
It is a chromatin protein
What are long non-coding RNAs?
Give an example
These are RNAs that have been spliced, capped and tailed
They associate with RNA and bring about change in chromatin structure and gene expression
XIST
What are the mechanisms of Long Noncoding RNA function?
They bind to regions of DNA, recruit proteins and act as:
Guide Scaffold Decoys Signal Enhancer
Describe the function of XIST long noncoding RNA
This RNA is synthesised, and binds to the DNA on the chromosome from which it was synthesised.
Once bound, it forms a loop with which proteins bind.
These proteins are histone methyl transferases PRCL
These proteins add methylation to the histone tails of this chromosome
What are the hall marks of a Barr body? (4)
- Low acetylation
- CgP island methylation
- H3K9me and H3K27me
- Long non coding RNA
Describe the mechanism of X inactivation
During development in the foetus (at gastrulation), each cell randomly inactivates on of the X chromosomes
This is so that each cell only produces only lot of X chromosome product (dosage compensation)
From then on, the same chromosome will be inactive in that cell and all its progeny
There is only one gene on the inactivate chromosome that is active: the XIST gene. It codes for a long noncoding RNA that coats that chromosome and recruits protein that increases the methylation of the histone tails
Describe how Barr bodies are a manifestation of epigenetic silencing (2)
They are a silent pocket at he periphery of the cell
They have no RNA pol activity
What is Rett syndrome?
What does the mutation lead to?
Rett syndrome is a x-linked neurodevelopmental disorder.
The mutation is a mutation in MECP2 which is a methyl binding domain protein
Describe the phenotype of Rett syndrome in females
Variable.
Heterozygous females can have very severity of phenotype because they may have 95% of the mutant X chromosome inactivates
Due to mosaicism
On a molecular level, where is methylation, and when does is it normally present?
- On the guanine on CpG islands of DNA - normally unmethylated
- Intergenic regions - normally silenced
- Repetitive elements - normally silenced
Methylation of the repetitive elements and intergenic regions corresponds to …
The integrity of the genome
