W9L2 Tues Epigenetic Flashcards
What is epigenetic
- change in gene expression without needing to change the DNA sequences by modifying the structure of the chromosomal region
What is chromatin
a mixture of DNA and proteins that form the chromosomes
What is nucleosome
the basic packing unit of genomic DNA built from histone proteins around which DNA is coiled
What is a histone
-a protein structure that provide structural support for chromosome
What is a histone tail
flexible regions that protrude from the nucleosome core
Post-translational Modifications (PTMs)
-covalent modification of specific amino acids in the Histone tail
-Many different type: methylation, phosphorilation, acetylation/ etc
Regulation of histone acetylation
§ Histone acetyltransferase (HAT) acetylate histone amino terminal tails = gene activation
§ Histone deacetylase (HDAC) deacetylate histone amino terminal tails = gene repression
§ Histone deacetylase inhibitors (HDACi) inhibit deacetylation (TSA – cancer treatment)
DNA Methylation
DNA maturation is adding a methyl group to DNA
§ Most CpG sites (>90%) are dispersed around genome at low densities + are usually methylated
§ CpG island: dense region of CpG sites usually unmethylated
Ø Unmethylated = transcriptionally competent
Ø Hypermethylated = blocked gene transcription
method of methylation
§ DNA methyltransferase (DNMTs) methylate DNA
§ Replication dependent methylation: DNA unwinds + replicates, new DNA strand is unmethylated → DNMT1
recognises hemi-methylated DNA + adds methyl groups (maintains methylation)
De novo DMNT3, add methyl group to unmethylated CpG
protein and process of methylation
§ De novo methylation: DNMT3A/3B/3L can add methyl groups to unmethylated DNA strands
§ Active demethylation: TETs
§ Passive demethylation: cell cycle loss with no DNMT1 maintenance
Non-coding RNA types
- microRNAs/siRNAs: 18-25 nucleotides, post-translational gene regulation, RNA interference
- Small RNAs: 20-200 nucleotides, template for telomere DNA< transcription regulation
- lncRNAs: >200 nucleotides, DNA imprinting, X-inactivation, DNA methylation, transcriptional regulation
Female X chromosome inactivation step
Sister non-coding RNA coating
→ H3 methylation + H2 ubiquitination
→ H4 hypoacetylation
→ histone variant incorporation
→ ATRX chromatin modifier enrichment
→ CpG island hypermethylation
Spatial heterogeneity
: every cell has a distinct epigenome due to cumulative environmental factors + stochastic influence
DNA methylation in foetus
§ Dynamic DNA methylome: once fertilised, both genomes are demethylated until blastocyst stage (almost unmethylated)
Ø After implantation, methylation occurs + remains
Ø In germ cells: second wave of demethylation creating egg-specific + sperm-specific methylation marks
Ø Environmental influences may affect genome during methylation + demethylation events
methylation and DOHaD
environmental exposure
→ sub-optimal intrauterine environment
→ molecular (epigenetic) disruption
→ metabolic/endocrine disruption +/or modified tissue function
→ foetal programming
→ predisposition
Postnatal maternal care: licking and groming
Ø Low licking/grooming: Nr3c1 gene promotor methylation = ↓expression = ↑corticosterone levels + anxiety
Ø High licking/grooming: methylation removed = ↑expression = ↓corticosterone levels + anxiety
diet and methylation bee example
Genetically identical bees can become workers or a Queen by being fed ‘Worker Jelly’ or ‘Royal Jelly’
-Switching off DNMT3 has the same effect!
Less DNMT3 = less DNA methylation = more Queen bees
Diet + DNA methylation
-One carbon donors (folate, Vit B2/B6/B12, choline) required to methylate
Ø Folate supplement: more offspring brown (due to ↑dietary methyl donors = agouti expression)
Why do we study methylisation
methylisation is highly stable, measured in any DNA sample, robustly measurable at genome/locus levels
DNA methylation during pregnancy
§ Widespread DNA methylation changes during pregnancy
§ Blood pressure of premature infants show large-scale epigenetic differences
The epigenetic clock and biological ageing
- Several recent studies have demonstrated age-associated changes in DNA methylation that occur independently of sex, tissue type, disease
- Methylation levels at ~350 sites accurately predict age
- Highly variable in early in life (Horvath, 2013)
Twin studies
Dizygotic (DZ group) vs Monozygotic (MZ group): relative role of genes and environment to phenotypic trait
If MZ intra class correlation > DZ ICC (evidence of genetic influence)
Ø Heritability for DNA methylation ~15-20% but mostly by environmental influences
Methylation quantitative trait loci (meQTLs)
SNP that influence level of DNA methylation at a particular CpG site
Ø SNP changes nucleotide = prevents transcription factor binding + DNMT1 methylates region
Ø Cis (91.5%) = nearby on same chromosome; trans = different chromosome
Ø ~50% of all CpG probes have a SNP that influences their level of methylation
Smoking and methylation
Prolonged exposure to smoking causes strong methylation
Ø Effect is tissue specific (CBMCs affected); 6073 CpGs with significance
Tools to study methylation
RNA-sequencing (gene expression high or low),
ATAC-seq (identify open chromatin/accessible for TF binding),
ChIP-seq (histone tail modifications),
WGBS (DNA methylation),
HiC (interactions b/w chromosomes)
Innate Immune Memory
(Trained Immunity)
An epigenetic process
§ Adaptive immunity: gene rearrangement to control expression, antigen dependent
§ Innate immunity: epigenetic modification of genes encoding immunological/inflammatory products; antigen independent
