Epigenetics Flashcards
What extra information does DNA hold?
Chemical modifications to the DNA and its associated histone proteins.
May also be heritable through mitosis and meiosis.
The dutch hunger example?
There was a famine and women who were exposed to the famine recovered, but later had children with long term health problems (diabetes, obesity, cardiovascular diseases etc).
Children’s children also had health problems. Something happened during pregnancy to re-programme development.
Cis-acting gene silencing mechanisms at imprinted gene clusters: looked at CpG islands in the Igf2 gene cluster in children conceived during the famine.
On the maternal chromosome, the unmethylated DMR binds the CTCF protein and form an insulator that clocks enhancers from activating the Igf2 and Ins2 (2 important genes upstream of the DMR).
Instead they enhancers activate a nearby promotor.
On the paternal chromosome the methylated DMR cant bind the CTCF , no insulator forms, the two genes are expressed only on this chromosome, and the methyl group from the DMR methylates and silences the other promotor.
Exposure to famine is associates with lower methylation of the IGF2 DMR, and may be related to a deficiency in methyl donors.
Fat male rat example?
High fat diet given to male rats, their body weight increased, their glucose tolerance was impaired and they got diabetes.
Their adult female offspring (and their offspring) had impaired insulin secretion, glucose intolerance and β-cell disfunction.
Rats from fat fathers were insufficiently methylated on the promotor of the Il13ra2 gene, resulting in downstream misregulation of 3000 other genes and b-cell disfunction.
Methylation was directly linked to the fathers obesity.
The methylation marks weren’t reset, and the fault was inherited only by females - maybe due to imprinting.
Fear inheritance in rats example?
Shock rats after exposure to certain smells, offspring generations down the line show instinctual fear without shocking.
Imprint behaviour on subsequent generations and alter development way down the line.
Bisulphate sequencing of the sperm DNA from conditioned males and naïve offspring, revealed CpG hypomethylation of the Olfr151.
They are inherited via the gametes and aren’t wiped.
Stains revealed a large increase in activity in the olfactory bulbs of offspring who’s parents underwent conditioning.
Rats licking and grooming example?
Early experiences shape later behaviours.
Mother rats lick and groom (LG) their young, LG babies grew up to be happy and normal. Babies without LG became depressed and had other problems, they had low levels of glutamate receptors in their brain.
Offspring of high LG mothers have an up-regulation of the GRM1 gene expression in the hippocampus. The gene encodes a glutamate receptor, and is caused by differential methylation of the genes promoter.
Low methylation = higher transcription = high LG.
High methylation = low LG.
An example of how male and female genes can behave differently?
Can see in pollination that male and female genomes contribute differently to seed development.
Describe chromatin structure?
Chromatin remodelling is important for gene expression.
“Active Chromatin” is characterised by histone acetylation and other changes, and “inactive chromatin” is the opposite.
“Heterochromatin” refers to large regions of the genome that are inactive for gene expression or silenced (telomeres, LCR, X chromosome inactivation, or genomic imprinting).
What do epigenetic modifications include?
Cytosine methylation of DNA.
Modifications to the tails of histone proteins.
What is cytosine methylation of DNA?
CG methylation can be symmetric or asymmetric
Symmetric methylation can be copied from the template strand by the machinery
Asymmetric methylation means that one of the new strands, the template strand has no methyls groups for the machinery to copy. They are maintained by information on associated histones and an RNA based mechanism (small interfering RNA copies of the template are in the cytoplasm that the machinery uses to read and impose the marks onto the DNA).
Heterochromatin is highly methylated
Repetitive elements are common near the centromere and this ensures that no genes are compromised during replication.
What modifications occur to the tails of histone proteins?
The amino terminal groups of the proteins extend beyond the nucleosome and are accessible for modification
They can be modified in different ways conferring transcriptional activation or inactivation: acetylation ubiquitination methylation phosphorylation.
Open/more transcription: e.g. methylate lysine 4
Closed/less transcription: e.g. methylate lysine 27
Different histone modifications are associated with different genes and transposons.
E.g. H3K27me3 (the trimethylation of histone H3K27, associated with shutting down transcription by inactivating promoter regions): the methylation can be conferred by Polycomb Recessive Complex 2 (PRC2). The methylation makes the DNA more compact and silences the genes. The complex has a methyltransferase function. In animals the silencing by PRC2 is maintained or stabilised by PRC1.
Roles of specialised non coding siRNAs in epigenetics?
Dicer-like (DCL) nuclease produces the siRNAs which bind to Argonaute (AGO) proteins to bring modifying enzymes like DRM1 and DRM2 to their DNA targets.
RNA polymerase IV dependent siRNA biogenesis: Pol IV transcribes a single-stranded RNA that is copied into a double-stranded RNA by RNA-dependent RNA polymerase 2 (RDR2) with the help of the chromatin remodeller CLASSY 1 (CLSY1). The dsRNA is processed by DICER-LIKE 3 (DCL3) into siRNA that are methylated at their 3’ end by HUA ENCHANCER 1 (HEN1) and incorporated into ARGONAUTE 4 (AGO4).
What are siRNAs?
small interfering RNAs
What marks active genes?
CpG islands mark the 5’ regions of active genes. At the beginning of the gene they clear methylation to allow transcription.
CpG islands are regions of low methylation and are associated with actively transcribed regions. They recruit methyl-transferases which remove the methylation and block methylation by preventing binding to histone tails.
What are DMRs?
Differentially methylated regions are upstream of regulators of active genes.
Genomic regions with different methylation statuses among multiple samples.
The identification of DMRs among multiple tissues provides a comprehensive survey of epigenetic differences among human tissues.
How does methylation reprogramming occur?
In the germline and the embryo. There is a cycle of erasion, with a purge of methylation occurring in the germ cells, and a re-establishment of the methylation in later stages.
Some genes escape the purge.
