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Epigenetics

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imissyou419's version from 2016-12-20 19:56

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What is epigenetics?HERITABLE CHANGES in gene expression that do not involve any change in DNA sequence (no DNA mutation) but modifications in the chromatin
What are the 3 types of epigenetics?1) modification of histone core proteins. 2) DNA methylation. 3) microRNA
Modification of histone core proteinscould be post-translationally modified -> phosphorylation, ubiquination, methylation, sumoylation, acetylation; can be associated with repressor or activation; includes chromatin remodelling proteins
DNA methylationgenerally at cystidines (cytosines?), usually associated with gene repression
MicroRNA + long non-coding RNAaffect transcription, silence genomic regions or alter RNA processing all leading to changes in RNA accumulation and expression (this is a epigenetic modification so can be inherited)
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Histonessmall, 100-300 amino acids which are mostly positive, each subunit has N-terminal tail that sticks out of the octomer core, these can be covalently modified to change DNA wrapping, each octomer is separated by linker DNA
DNA wraps around histones2.5 times, w/ linker region of ~150 bp = nucleosome
Histone regions2H2A, 2H2B, 2H3, 2H4 = octomer
Writerse.g. HAT, HMTS, PRMT; proteins add modifications along tail
Readerse.g. bromodomains, chromodomains, Tudor domains; recognize codes and exert their function on transcription or chromatin remodelling, etc
Eraserse.g. HDACs, KDMs (lysine demethylases - JARID1 and Jjmk3); remove modifications
HISTONE ERASERS NOT PASSIVE B/C IT'S HISTONESSS (only passive for DNA)
Histone acetylation catalyzed by what and how and what does it docatalyzed by enzyme family of histone acetyl transferases (HATs) - transfers an acetyl from acetyl-coA to histone tails; acetylation causes DNA to be unwound to allow for transcription
HAT A enzymesactive only in nucleus
HAT B enzymesactive in cytoplasm and modify new histones prior to incorporation into nucleosomes
Many transcription factor carryhistone acetylation ability / deacetylation ability and bromodomains so can acetylate DNA and use bromodomain to open up chromatin and carry out function depending on what transcription factor is (TF can get in or not)
HDACsremove acetyl group from histones;
HDACs are upregulated in cancer -> shut down various regions of genome (tumour suppressor genes) and allow oncogenes to take over
Class I HDACs (1-3,8)located in nucleus only
Class II HDACs (4-7,9,10)active in nucleus and cytoplasm and shuttle between compartments
Do HATs and HDACs directly bind DNA?No, they are recruited by transcription factors (inc. nuclear receptors)

Presence of ligand, heterodimer nuclear receptor complex binds to co-activator complex and recruit HAT, HMT to open up DNA to get transcription
Absence of ligand, heterodimer nuclear receptor binds to co-repressor and recruit HDACs
Histone methylation catalyzed by what and how and what does it dohistone methyltransferase (HMT) methylate arginines or lysines by transferring a methyl group from donor SAM; carried out by the SET domain regions; methylation can be both an active or repressive mark depending on residue marked
Lysine methyltransferases (KMT)MLL for H3K4 (writer), PRC2 for H3K27
Lysine demethylases (KDM)JARID1 for H3K4 (eraser), Jmjd3 for H3K27
Trimethylation of H3K4active mark
What catalyzes methylation of H3K4?MLL
Trimethylation of H3K27repressive mark
What catalyzes methylation of H3K27?PRC2 (specifically EZH2)
Enhancer of Zeste Homologue 2 (EZH2)Part of PRC2, establishes trimethylation of H3K27 ONLY, H3K27Me3 is associated to parts of the genome that are either weakly transcribed or silent, both upregulation and inactivation of EZH2 could have deleterious consequences: - upregulated in cancer (b/c cancer is proliferating and actively methylates DNA to silence tumour repressor regions), somatic LOF mutation in leukemias, necessary for proper specification of liver vs. pancreatic fate in development (silence all genes that dictate other fate)

Generally not expressed in high levels in adult tissue, high levels in proliferating tissue because once it causes methylation, does not need to be there anymore
What happens if you mutate EZH2?do not get methylation event -> leukemias
What are the backbone of PCR2?EZHZ with SET domain, EED, SUZ12
Transition from euchromatin to heterochromatinH3K4Me3 (active genes) -> H3K27Me3 -> H3K9Me3 (heterochromatin)
Bromodomainbinds acetylated lysines on histones (reader), modify chromatin
Chromodomainbinds methylated lysines on histones (reader), modify chromatin
SAINT domainsbinds unmodified histones (reader), modify chromatin
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Why have both repressive and active marks?exists on developmentally important genes (turn on genes for process and off genes not for process) or immediate response gene (rapidly turned on or off), the genes are "primed"
Why is this level of control for epigenetics?
(heterochromatin + euchromatin)
allows specific type of genes to be "fixed in" (genes start off as open and become euchromatin or heterochromatin), prevent improper activation of genes (limit effects of activators and enhancers that would be needed if it was all euchromatin), keep gene in a "steady" state (genes inactive but primed), provides link b/w environment and gene regulation (respond rapidly to environmental change)
Babies born to mothers starved the first few months of pregnancy had higher rate of obesity + increased risk for diseases
+ their children had higher risk too
improper modification of histones (could be addition or loss of methylation) due to environmental stress received in fetus so they are predisposed to disease (different gene expression), that predisposition to disease is inherited so their children is predisposed to react certain way to environmental stress = disease

Methylation affected by famine because decreased folic acid
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DNA methylation functiongenerally gene repression
DNA methylation entailrecruitment of factors that allow for inheritance of histone modifications, include interacting with histone modifying enzymes or preventing binding of transcription factors, inactivation of X chromosome in females, imprinting - monoallelic gene expression of maternal or paternal genes, repression of DNA translocation, repression of gene expression
DNA can be modified by methylation ofcytosines (functional relevance of non cytosine methylation not clear)
How much of the genome is methylated?4.25% of TOTAL CYTOSINES in genomic DNA are methylated, 67% of CpGs are methylated, 99% of DNA methylation occurring on CpG dinucleotides
CpG islandscompose 1% of genome, 10 fold higher frequency of CpG dinucleotide than the rest of the genome, originally defined as genomic region with 200 bp in size with C + G content of 50% and an observed CpG/expected CpG > 0.6, often associated with promoter regions of genes, >50% of all mammalian genes associated with CpG islands, actively protected from DNA methylation to allow for appropriate regulation of transcription (CpG islands not methylated when at promoter or enhancer)
CpG island containing promoter hypomethylated (lack of methylation)permissive of transcription
CpG body and repetitive DNA-hypermethylateddownstream or intergenic, repressed
What happens to methylation in cancer?
How do therapeutic drugs work?
Overall DNA methylation levels are reduced (hypomethylation), so transcriptionally active. Tumor suppressor genes are repressed (hypermethylated through DNA methylation & histone methylation)

Most drugs (HDAC inhibitor, DNMT inhibitor, etc) are repressing a repressor so activate those tumour suppressed genes
Given to target proliferating cells (cancer) and not normal cells
DMNT1maintains previously methylated DNA, copy DNA methylation patterns during DNA synthesis onto new strand + repair of DNA methylation patterns (only active in replicating cells)
What does 5-azacytidine do to DMNT1?inhibit DMNT activity in PROLIFERATING cells (good to use 5Aza in cancer because cancer is proliferating and hypermethylate tumour-suppressing genes so get rid of methylation + works in proliferating cells so want to kill proliferating cancer cells through un-methylation, target whole genome so don't use if it's not cancer)
DMNT3A and DMNT3Bpatterns of methylation are established during DIFFERENTIATION AND DEVELOPMENT (wipe out DNA methylation and re-establish b/c want pluripotency, capable of methylating native DNA, regardless of whether the DNA is in a replicative state or not
DNMT3LDMNT3A and B regulatory factor - acts as DNA repressor or activation (activate by preventing DMNTs from binding to DNA through binding proteins so don't methylate the DNA)
Passive demethylationpassive - based on cell division and inhibition of DMNT1 (this is how the cell gets rid of a lot of DNA methylation during development)
Active demethylationremoval or conversion of methylcytosines and with base excision repair or nucleotide excision e.g. Tet1 protect CpG islands and prevent DMNT methylation, if CpG island methylated, repair it by converting it to hydroxylmethylated or just go in and remove methylated cytosine by breaking DNA, hydroxylmethylated CpG can be removed through active demethylation to re-establish demethylated area (can either base excision repair (remove single cytosine) or nucleotide excision repair (take out small stretch of nucleotides))
How does DNA and histone affect each other in epigeneticsHistone methylation (H3K9 and H3K27) can help direct DNA methylation, and DNA methylation may help modify histones after DNA replication
H3K9Me and H327Me recruitDMNT3A/B (NOT DMNT1)
DMNT recruitMeCP2 & MBD2 (methylcytosine binding protein), recruit HDACs & HMT (H3K9)
What is the methyl donor for DNA methylation?SAM (same for methyl donor for histone methylation)
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