W9L2 Tues Epigenetic

Question 1

What is epigenetic

Answer 1

• change in gene expression without needing to change the DNA sequences by modifying the structure of the chromosomal region

Question 2

What is chromatin

Answer 2

a mixture of DNA and proteins that form the chromosomes

Question 3

What is nucleosome

Answer 3

the basic packing unit of genomic DNA built from histone proteins around which DNA is coiled

Question 4

What is a histone

Answer 4

-a protein structure that provide structural support for chromosome

Question 5

What is a histone tail

Answer 5

flexible regions that protrude from the nucleosome core

Question 6

Post-translational Modifications (PTMs)

Answer 6

-covalent modification of specific amino acids in the Histone tail
-Many different type: methylation, phosphorilation, acetylation/ etc

Question 7

Regulation of histone acetylation

Answer 7

§ 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)

Question 8

DNA Methylation

Answer 8

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

Question 9

method of methylation

Answer 9

§ 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

Question 10

protein and process of methylation

Answer 10

§ 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

Question 11

Non-coding RNA types

Answer 11

1. microRNAs/siRNAs: 18-25 nucleotides, post-translational gene regulation, RNA interference
2. Small RNAs: 20-200 nucleotides, template for telomere DNA< transcription regulation
3. lncRNAs: >200 nucleotides, DNA imprinting, X-inactivation, DNA methylation, transcriptional regulation

Question 12

Female X chromosome inactivation step

Answer 12

Sister non-coding RNA coating
→ H3 methylation + H2 ubiquitination
→ H4 hypoacetylation
→ histone variant incorporation
→ ATRX chromatin modifier enrichment
→ CpG island hypermethylation

Question 13

Spatial heterogeneity

Answer 13

: every cell has a distinct epigenome due to cumulative environmental factors + stochastic influence

Question 14

DNA methylation in foetus

Answer 14

§ 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

Question 15

methylation and DOHaD

Answer 15

environmental exposure
→ sub-optimal intrauterine environment
→ molecular (epigenetic) disruption
→ metabolic/endocrine disruption +/or modified tissue function
→ foetal programming
→ predisposition

Question 16

Postnatal maternal care: licking and groming

Answer 16

Ø Low licking/grooming: Nr3c1 gene promotor methylation = ↓expression = ↑corticosterone levels + anxiety
Ø High licking/grooming: methylation removed = ↑expression = ↓corticosterone levels + anxiety

Question 17

diet and methylation bee example

Answer 17

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

Question 18

Diet + DNA methylation

Answer 18

-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)

Question 19

Why do we study methylisation

Answer 19

methylisation is highly stable, measured in any DNA sample, robustly measurable at genome/locus levels

Question 20

DNA methylation during pregnancy

Answer 20

§ Widespread DNA methylation changes during pregnancy
§ Blood pressure of premature infants show large-scale epigenetic differences

Question 21

The epigenetic clock and biological ageing

Answer 21

• 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)

Question 22

Twin studies

Answer 22

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

Question 23

Methylation quantitative trait loci (meQTLs)

Answer 23

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

Question 24

Smoking and methylation

Answer 24

Prolonged exposure to smoking causes strong methylation
Ø Effect is tissue specific (CBMCs affected); 6073 CpGs with significance

Question 25

Tools to study methylation

Answer 25

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)

Question 26

Innate Immune Memory
(Trained Immunity)
An epigenetic process

Answer 26

§ Adaptive immunity: gene rearrangement to control expression, antigen dependent
§ Innate immunity: epigenetic modification of genes encoding immunological/inflammatory products; antigen independent