30th Jan - Epigenetic Regulation Flashcards
(33 cards)
What is epigenetics?
The study of modifications that alter the phenotype of the cell without altering the genotype. heritable traits over rounds of cell division and sometimes transgenerationally
What is the function of DNA methylation?
Long term Inhibition of transcription, mainly to keep the junh (transposons, repetitive elements and endogenous retroviruses) quiet
Which base is methylated in eukaryotes?
Cytosine
Which base is methylated in prokaryotes?
Adenine
Where does methylation occur in eukaryotes?
At CpG dinucleotides
When is methylation reversible in a eukaryote?
During embryogenesis
Give three examples of DNA methyltransferases
Dnmt1, Dnmt 3a and Dnmt 3b
Outline the function of Dnmt1
It methylates hemi-methyalted DNA after replication therefore copying the epigenetic code from the template strand thus is replication dependent
Outline the function of Dnmt 3a and 3b
It methylates DNA de novo i.e. it methylates one strand of DNA, Dnmt1 then methylates the other strand
What Is the evidence for DNA methylation maintaining genomic instability?
5-azacytidine
- -Cytosine analogue that can’t be methylated
- -When added to the cells it dilutes DNA methylation through each round of cell division
- -Loss of DNA methylation leads to reactivation of endogenous retroviruses
Dnmt1 KO mice
- -Retain only 10% of normal activity
- -Develop aggresive T cell tumours due to trisomy of chromosome 15
hypomethylation is a common trait in cancer
How was it demonstrated that coat colour controlled in mice is controlled by DNA methylation?
Agouti = yellow pigment
Used a series of genetically identical mice, and added an endogenous retrovirus which inserts above the Agouti gene.
In yellow mice most CpG islands in Agouti are unmethylated
In pseudoagouti mice every CpG in the Agouti gene is methylated –> brown mice
Gradient of colours dependent upon the level of methylation
What percentage of CpG dinucleotides are methylated in the mammalian genome?
> 50%
Why are cytodines under-represented in the mammalian genome?
Over time cytodines can be converted to thymidines. Most of these are repaired however some will escape over the course of evolution –> loss of approx 3/4 of CpG dinucleotides
Where are CpG dinucleotides most common?
Around 5’ end of active genes
What are CpG islands?
Regions with >50% CpG content about 1-2kb in length usually located at the 5’ end of the genome, and are resistant to DNA methylation
How does DNA methylation lead to long term silencing?
If Methylated CpG > unmethylated CpG –> Gene off
As the methylation is recognised by methylated CpG binding proteins that act as transcriptional repressors by recruiting histone modifying enzymes
Give an example of a methyl CpG binding domain
Mecp2
MBD2
MBD1
Give an example of a Zn-finger protein which is a methyl CpG binding protein
Kaiso
ZBTB4
ZBTB38
What is the function of NuRD?
The Nucleosome remodelling and deacetylase complex integrates DNA methylation and histone modification activities
What are the constituent proteins of NuRD?
the histone deacetylase core proteins HDAC1 and HDAC2,
the histone-binding proteins RbAp46 and RbAp48,
the metastasis-associated proteins MTA1 (or MTA2 / MTA3),
the methyl-CpG-binding domain protein MBD3 (or MBD2)
the chromodomain-helicase-DNA-binding protein CHD3 (aka Mi-2alpha) or CHD4 (aka Mi-2beta).
What are the two histone modifying enzymes in the NuRD complex?
HDAC 1/2
Mi2beta twists nuclesomes either further apart or closer together
In which cells does hydroxymethylcytosine predominantly occur?
Brain and stem cells
What is hydroxymethylcytosine?
A stable intermediate in the demethylation process
What is the function of TET proteins?
Ten-eleven translocation proteins plays a role in the active demethylation of cytidine
