epigentic applications Flashcards
name 2 ways to study epigenetics
DNA-protein interaction (histone modifications)
DNA methylation sequencing
Non-coding RNA sequencing
explain how DNA-protein interaction (histone modifications) is used to study epigenetics
- Crosslink DNA-proteins & isolate
- immunoprecipitate with specific antibody
- Remove crosslinks & purify DNA
- DNA sequencing
Peak calling: identify regions of the genome associated with specific histone modifications
explain how DNA methylation sequencing is used to study epigenetics
- Bisulfite treatment: conversion of non-methylated Cytosine into Thymine
- Bisulfite sequencing analysis: ratio of C/T = level of original methylation
explain how Non-coding RNA sequencing is used to study epigenetics
- Extract total RNA
- Enrich ncRNAs (size selection, chemical enrichment. mRNA + rRNA depletion etc)
- High throughput sequencing
- Align to genome or ncRNA sequences
- Annotate & quantify ncRNAs
4 reasons to study epigenetics
Regulation of development
Response to environment
Contributions to phenotypic plasticity
Disease risk
2 examples of Response to environment reason to study epigenetics
- Twin study: their shared epigenetic marks they were born with gets modified as they get older due to environmental effects
- Animal study (bees): if royal jelly nutrition is high you get lower DNA methylation (queen bee) + if royal jelly nutrition is low you get higher DNA methylation (worker bee)
explain why epigenetic contributing to phenotypic plasticity is a reason to study epigenetics
- Epigenetic modifications can induce stable changes in gene expression
-during an individual’s lifetime (mitotic inheritance)
-potentially heritable - Development of tolerance to environmental stressors e.g. Metal exposure in Rice altered methylation patterns which were heritable - increased metal tolerance in progeny
- Rapid adaptation to a new environment
example of Disease risk being a reason to study epigenetics
The agouti mouse as a biosensor for nutritional and environmental effects on the foetal epigenome and disease risk
- agouti gene in one offspring is methylated (not transcribed) while the agouti gene in the other offspring is non methylated causing it to transcribe
- non methylated mouse shows yellow fur, obesity, diabetes + prone to cancer when exposed to environmental effects like poor diet and alcohol
name 4 examples of epigenetic case studies
- Why identical twins are not actually identical
- Stress memory inplants improves drought tolerance
- Inherited fear behaviour in rats
- The Dutch Hunger Winter
explain the stress memory case study of epigenetics
- many different interacting mechanisms of chromatin modification
- In this case drought activation = modification of histone protein - allows the gene to be read and the plant to respond to the environmental stress
- this stress memory and how to deal with it can be inherited
- Benefits:
>protection against future stress
>local acclimation to changing environment
Costs:
>resource intensive
>potentially reduced growth or yield
explain heat shock proteins in the stress memory case study of epigenetics
- Important proteins help protect and recover cells after thermal stress (immune response also)
- Main classes: Heat Shock Protein (HSP) 70, HSP90, HSP27
- Genetic regulation- Heat Shock Factors activated by thermal stress -> Increased HSP expression
- Epigenetic regulation- Promoter regions methylated -> affects (likely reduces) HSP expression
- Histone modification- histone modifications of H2B and H3 -> again affects HSP expression
explain the Inherited fear behaviour in rats case study of epigenetics
- Fear conditioning in rat: Electric shock + odour of Acetophenone
- Conditioned male mated with normal female – offspring also showed fear when smelling Acetophenone
- In the rats that have been treated: hypermethylation in certain gene = overexpression of the gene
- This gene also found in sperm cells - that’s how response has been inherited
explain the Dutch Hunger Winter case study of epigenetics
- 1944-1945 dutch were completely isolated during war – fear, no food
- Some people were still pregnant:
>Famine late in gestation = smaller birthweight -> But no increase in later-life health problems
>Famine early in gestation: normal birthweight -> increased health problems incl. obesity, diabetes, coronary heart disease, schizophrenia) -> Altered birth weight & epidemiology in grandchildren (inherited) - Very early development is especially sensitive (epigenetic re-programming)
- Inherited due to multigenerational exposure: if we are pregnant we have 3 generation inside us – ours, the foetus’ and the foetus’ reproductive cells
why was there no later-life health problems in late gestation but an increase in health problems in early gestation
2 key points where epigenetic reprogramming happens = fusion + formation of gamete cells - Famine early in gestation would be subject to epigenetic reprogramming, whereas it would not effect late gestation
