Trigger 8: Basic epigenetics Flashcards
define what the epigenome is
the REVERSIBLE regulation of gene expression, mediated primarily through changes in DNA methylation
DNA determines
which mRNA is synthesises
Epigenetic determines
how much mRNA is made, where and when it is synthesised
how can genes without mutations cause mutations
due to epigenetic editing increasing or decreasing gene expression
epi means
above
the epigenome control
gene accessibility
the epigenome does not control
the genetic code
Two main types of chemical modifications
- chemical modification of the genome
- histone modification
genomic modification
through methylation and demethylation
histone modification through
- acetylation
- deacetylation
- methylation
- phosphorylation
epigenetic modifications act as switches
turning genes on/ off, decreasing/ increasing expression
epigenetic explains why cells of identical phenotype end up as
neurones, muscle and skin
why is the epigenome importnant
causes cellular differentiation during foetal development- meaning that although all cells have the same genome, they are not the same due to differences in the epigenome
different cell types are characterised by
different epigenomes
haploid genome contains how many BP
3 billion (6 billion in diploid)
all the base pairs are packaged into
23 chromosomes (46)
DNA is complexed with
histones
Nucleosomes consist of
8 histones around which DNA wraps 1.65 times
DNA methylation involves the methylation of what
CpG islands
CpG islands
parts of the genome rich in Cytosine and guanine
C and G order
C must come before G
which part of the CpG island is methylated
Addition of methyl group to C-5 position of cytosine residues.
Most cytosine methylation occurs in the sequence context
5‘-CG-3’
when methyl is added to cytosine it becomes
5-methyl cytosine
human genome is not
methylated uniformly- contains regions of unmethylated segments interspersed by methylated regions.
% of 5-methylated cytosine found in the genome
4%- primarily at cytosine–guanine dinucleotides (CpGs)
CpG islands (CpG rich regions) are found in how many promoter regions
50%
methylation within promoter regions correlates with
transcriptional silencing
methylation dysregulates gene transcription through
inhibition of transcription factor binding either directly or via altered histone acetylation
which enzymes catalyse methylation of CpG island
DNA methyl transferases
DNA methyl transferases
DNMTs
where does the methyl group that DNMTs transfer to CpG island comes from
S-adenosyl methionine (SAM)
when methyl is removed from SAM by DNMT it becomes
SAH
SAH
S-adenosyl homocysteine
Summary of DNA methylation
DNMT1 transfers methyl group from SAM to CpG island.
SAM–>SAH
which cytosine has methyl added
cytosine on 5th positiion
when cytosine has methyl added it becomes
5 methyl cytosine
therefore when lots of methylation of on CpG islands…
genes turned off due to TFs not being able to bind
how many types of DNMTs
4
methylation is an important mechanisms for
maintaining gene expression e.g. when cells differentiate they will not use all of their genes
which DNMT maintains normal patterns of methylation
DNMT1
de novo methylation
when genes are turned off and cause disease
which DNMTs are ‘de novo methylases’
DNMT3a and DNMT3b
DNMT1 requires a
heme-methylated DNA substrate and will faithfully reproduce the pattern of DNA methylation on the newly synthesised strant
DNMT3a and DNMT3b
all add methyl groups to CG dinucleotides which are previously unmethylated on both stands
- re-eastablish methylation patterns
DNMTs stand for
DNA MethylTransferases
both establishment (DNMT3B) and maintenance (DNMT1) ae
crucial for development
mice deficient in DNMT3B or DNMT1
embryonic lethal
mice deficient in DNMT3a
die within 4 weeks
DNMT1 important during
DNA replication- to ensure DNA is methylated in the same places
5 hydroxy methyl cytosine (5hmC)
is prevalent in embryonic stem cells and in the brain and plays a role in promoting gene expression
How does 5hmC promote gene expression
conversion of 5mC (methylated cytosine- created by DNMTs) to 5hmC by TETs blocks repressive proteins that would typically be recruited to 4mc
5mc
5 methyl cystosine
5 methyl cytosine is produce by
DNMT
- Methyl group removed from SAM and added to cytosine on CpG islands
outline active demethylation cycle
1) DNMT catalyses production of 5-mC from cytosine- repressing transcription and silencing genes
2) 5-mC is converted to 5hmC by TET, which then gets converted by another TET to 5-fC
3) 5-fc is converted to 5-caC
4) TDGBER convers 5-caC to cytosine
passive demethylation
occurs due to absence of methylation of newly synthesised DNA strands by DNMT1 during several replication rounds
active demethylation
mediated by multiple enzymes and can occur independent of DNA replication (TET and TDGBER)
