18.01.20 Epigenetics Flashcards
Give an overview of epigenetics.
- Heritable and transient changes in gene expression that do not alter the primary DNA sequence.
- Epigenetic effects persist throughout an organism’s lifetime and are passed on to multiple generations.
- Switches genes on/off → determines how proteins are transcribed → contributes to variable expression in different cell types.
- Essential for development and many normal cellular processes.
5 .Changes in these factors can play a critical role in disease.
- Initiated and sustained by at least three mechanisms: DNA methylation, histone modification and RNA-associated silencing.
Give three different mechanisms of epigenetic gene regulation.
- DNA methylation
- Histone modification
- Non-coding RNA
Give two types of histone modification
acetylation/deactylation
methylation/demethylation
Give an overview of DNA methylation
Involved in imprinting, X-chromosome inactivation, suppression of repetitive elements and carcinogenesis.
Helps maintain genome stability and prevent illegitimate recombination.
Role in determining the conformation of chromatin and holds the key to the heritability of epigenetic changes.
A signal that regulates gene expression (generally suppresses)
How are genes methylated?
Biochemical process: addition of methyl group (CH3) to the C5 position of cytosine to form 5-methylcytosine (5MeC).
Almost entirely restricted to cytosines of CpG dinucleotides - results in two methylated cytosines diagonal to each other on opposing DNA strands.
In mammals ~70% of all CpG dinucleotides are methylated.
Carried out by DNA methyltransferase (DNMT) enzymes - uses S-adenosylmethionine (SAM) as the methyl donor (results in S-adenosylhomocytosine).
Animals deficient in DNA methyltransferase activity die at various stages of development.
Added methyl group acts as a signal that is recognised by specific MeCpG-binding proteins.
Concentrated on repetitive sequences (e.g. pericentric heterochromatin and dispersed transposons), sporadically distributed in genes and intergenic sequences.
High proportion gene promoter CpGs (CpG islands) stay unmethylated → less prone to deamination.
Which enzymes are involved in DNA methylation?
DNMT1
DNMT3A
DNMT3B
Describe the role of DNMT1 and its associated proteins.
Maintenance methylase: copies the methylation from hemimethylated DNA to its new partner strand after replication - throughout life of organism.
Associated with: PCNA (replication forks), methyltransferases, HP1 (heterochromatin), methyl binding proteins
Describe the role of DNMT3A and DNMT3B and their associated proteins.
De novo methylase: adds initial pattern of methyl groups. Expressed mainly in early embryo
Associated with: Histone methyltransferases; histone deacetylases
What is the role of DNMT3L?
non-functional DNMT but does help stimulate de novo methylation and is thought to be required for the establishment of maternal genomic imprints.
What is the role of TET1-3?
TET 1-3 (Ten-eleven translocation) enzymes: converts 5MeC to 5-hydroxymethylcytosine (5hmC) in what is proposed to be first step in an active demethylation pathway. Important during development and tumorigenesis.
When do rapid changes in DNA methylation occur (draw diagram)?
- Gametogenesis - substantial de novo methylated genomes in the sperm and egg.
- Early embryogenesis - wave of genome-wide demethylation at the pre-implantation stage. This epigenetic reprogramming erases adult methylation patterns.
- Post-implantation - large-scale de novo methylation by DNMT3A and DNMT3B.
How does the position of DNA methylation influence gene control?
In immediate vicinity of transcriptional start site > blocks initiation.
In gene body > does not block and may stimulate transcription elongation. May effect splicing.
In repeat regions > important for chromosomal stability.
Describe Methyl-CpG-binding proteins.
5MeC pairs with guanine in the same way as unmodified cytosine but the methyl group acts as a signal recognised by specific MeCpG-binding proteins.
These can then recruit other proteins associated with repressive structures such as histone deacetylases (HDACs) and have a role in regulating chromatin structure and gene expression.
Demethylation relaxes chromatin allowing histone acetylation and binding of transcriptional complexes.
Humans have 5 MeCpG-binding proteins: MBD1-4 and MECP2.
Loss-of-function of MECP2 causes Rett syndrome (X-linked).
What is histone modification and its effect?
Histones are proteins that are the primary components of chromatin- the complex of DNA and proteins that make up chromosomes (see notes on DNA structure).
The N-terminus of histone molecules protrude from the body of nucleosomes.
Chemical modifications of amino acids in these ‘histone tails’ are major determinants of chromatin conformation and consequently influence DNA transcription.
In a compact form it is active and the associated DNA can be transcribed.
If chromatin is condensed (inactive), DNA transcription does not occur.
What is acetylation/deacetylation?
Histone modification
Acetylation/Deacetylation – adds/removes an acetyl group (COCH3) to free amino groups of lysines or arginines.