Epigenetic inheritance Flashcards
Describe modes of epigenetic inheritance
Mitotic stability through growth and dev - through cell division
Transgenerational stability may involve transmission to gametes - propagate through germ lime
What does epiegnetics help maintain
Cellular memory identity during development = memory
Genes associated with multi potency turn off as differentiate,and lineage specific genes turn on
Maintained in stable way through multiple cellular divisions
Can epigenetic mechnanisms confer transgenerational stability
Epigenetic change in parent —> potentially transmitted to germline —> inherited by offspring potentially
What s dnmt1 involved in
Maintainance - inheritance of dna meth
Propagates by targeting hemi methylated cpg products
What makes dnmt1 a maintenance methyl transferase
What does it act like this - targets specifically
What is preferred substrate for dnmt1
In vitro = hemi methylated dna
Intrinsic property of dnmt1 domain
What does dnmt1 associate with - sites
Sites of dna rep in s phase via dna interaction - physically attached to dna rep
Biological properties that ensure it plays a role
Protein-protein interactions that Link dnmt1 to site of dna rep, to replication fork
What does dnmt1 associate with - domain
Uhrf1, which specifically bins hemi methylated dna
Uhrf1 has specific recognition ability
Other factors that help promote maintenance activity
Uhrf1= sra
Describe h3k9me and how it helps dnmt1
Helps direct dnmt1 action and can reinforce dnmt1 function by recruiting Uhrf1
Describe what makes dnmt1 a maintenance methyl transferase general pathway
Uhrf1 specifically recognizes hemimethylated dna
Urhf1 links to histone methylation site
Brings it preferentially to h3k9me
Strong marker constitutive heterochromatin
Specifically wants lots of maintenance to keep stable bc many meth
Helps maintain dna meth through cell divisions
Describe ideas of maintenance of poly comb repression - questions
Do histone mods get copied during cell division
What role does h3k27me and/orh2aub1 have in maintenance - associated with polycomb repression
Is there a mechanism for copying this modified histone analogous to copying of cpg methylation of dna - copy modified hsiorne and transmit during cell devision
How do poly comb proteins work together - gen
Strong evidence of copying mechanism
Polycomb protein complexes regulate one another through positive feedback
Describe poly comb protein “loop”
Self propagating feature of polycomb repression
Prc2 = puts on h3k27, and recognizes h2AUB
Prc1= recognizes h2k27 and puts on us
Structure of complexes means that histone modification by one leads to recruitment of other, can lead to modification binding cycles = positive feedback loop
What does the positive feedback loop between polycomb protein complexes maybe account for
Spreading of complexes on chromatinn
Also important part of models of inheritance through cell division
Domains of transcriptional repression, can spread along histone - prc1 and 2
Describe copying mechanism - gen
Suggested by presence of reader and modifier domains within same complex or 2 related complexes
Describe copying mechanism - specifics
Ex = prc2, has capability, both domains
More general mechanism forcopying histone mods
Also suvar39
Describe copying mechanism - specifics K27me
On prc2
Ezh2 = h3k27me
And the Eed can read k27me
Just prc2 alone has potential to go through cycles of modifying histones then recruiting another prc2 complex
= can spread mods across chromosomes
Describe copying mechanism - specifics H3k9 me
Suvar39
H3k9me put on by set domain
Another part of protein = chromodomain can read k9me
= potential for repeated cycles of h3k9
= can spread mods across chromosomes
What happens to his tones during dna replication
Daughter dna strands carry a combo of old and new nucleosomes - potential for copying mechanism exists
Replication fork = ahead-pre existing core histones h3 and h4, behind rep fork = combo of new and old nucleosomes, that get assembled on new daughter stands
Mixture, new histones brought in do not have same mods of old
Have to copy on both leading and lagging strand
Is there a hsitone medication copying mechanism that occurs during dna replication
Copying occurs from previously methylated old histones to unmethylated new histones
Old histones = have to be re deposited locally
Interaction between old histones and components of replication machinery ensure this
Prc2 associates with an old nucleosome = k27me, then if new nucleosome near = will copy mods, since ezh2 - mototic stability h3k27 - will methylated next to it
New and old nucleosomes must be clsoe for this to work
Cell has to hang on to old histones = template for new
Describe strong evidence for a copying mechanism - Gen
From prc2 dinculesome structure = studies
Describe strong evidence for a copying mechanism - Whole thing
Dinucleosome is composed of one monomer unmodified = substrate and one monomer that already has h3k27me3
Eed subunit bound to h3k27me3 nucleosome, ezh2 methyl transgressed bound to substrate nucleosome
Binding of Eed to h3k27me activates enzymatic activity of complex
Prc2 loves theses substrates
Describe strong evidence for a copying mechanism - Domains/complexes
Prc2 = assembled complex, on pieces of chrosmoems with 2 nucleosome, where one nucleosome has h3k27me and other doesn’t
Set = catalytic domain fo ezh2 - set binds and methylates unmethylated one and ezh2 binds h3k27me3
Describe transgenerational epigenetic inheritance
In plants, smaller eukaryotes
Not exact evidence in humans
What does intergenerational mean
Due to initial indirect exposure of gametes in F0
Parent = give stress and measure effect on parent, is it transmitted to newer gens, even when not given same stress?
What does transgenerational mean
Due to transmission of an epigenetic change to gametes independently of initial exposure
Describe where we have to look for males and females. = to see transgenerational epigentic inheritance
Male = if subject germline to stress, = would pass on so look after F2
In females = affects parent, embryo and GERMLINE of embryo = F1, F2 so look after F3
Describe how we think about natural selection - inheritance of acquired characteristics
Regular natural selection = tall giraffe will win and shor will die, so only tall giraffes carry on, natural genetic variation expressed in population
Epignetic = make themselves taller so can eat, animals become bigger, animals might have ability to change in response to stress
Describe evidence for transgenerational epigenetic inheritance model systems- maize
Tranposon insertion in colour genes promoters, variable dna meth in tranposon leads to variegated expression, stable for generations-inherited in stable way
Describe evidence for transgenerational epigenetic inheritance model systems - mice
Isolated Cases ex =
Makes mice lighter coat, very sensitive to methylation state, if becomes more methylated = reduce transcription agouti gene = dark mouse
Extent of methylation regulates expression fo agouti genes
Methylation state of IAP (transposon derived) in agouti promoter can be maintained even through germline development, controls coat colour and drives transcription of agouti gene
Describe epigenetic transmission in mammals
Epigenetic transmission via dna meth is rare in males bc of epigenetic reprogramming in germline
Where all dna meth wiped out but somehow these elements maintain methylation
Describe epigenetic transmission in plants
More common in plants as germ cells arise from somatic cells, reprogramming is incomplete
What may be key drivers of transgenerational effects
Transposons may be actively resistant to reprogramming = may be key drivers of trasngernational effects
Methylation state stably maintained over generations, in germlines
Describe non gametic epigenetic inheritance - in rat generally
Inheritance of maternal care behaviour phenotype, stable effect
Low licking and grooming = high corticosterone levels, high anxiety
High licking and grooming = low corticosterone and low anxiety
Bc low glucocorticoid receptor = methylation of promoter here, methylation response to stress level
Female pups inherit and can transmit to daughter
Not germline effect
Describe non gametic epigenetic inheritance in rat - what does low maternal care lead to
Cpg methylation in promoter of genes for glucocorticoid receptor in hippocampus in pups
Describe non gametic epigenetic inheritance in rat - stress response
Blocks tf binding and lowers expression and leads to actiovation of hormonal stress response
Stress response maintained Into adulthood and the female pup transmit it to their pups
Describe non gametic epigenetic inheritance in rat - what is it an example of
Temporal stability of a gene expression state - mechanism?
Maternal care phenotype passed on through gens but no evidence that involves germline transmission
Describe evidence for intergenerational epigenetic inheritance of effects of environmental exposure in humans
Dutch famine 1944:
Male babies born to mothers who lived through the famine were small, this effect was noted in their children as well after famine was over
Kids much smaller during famine, also effects next Gen (no famine) = potential epigenetic effect
Describe intergenerational inheritance of effects of environemtal exposure exp
Evidence that changes in paternal diet/metabolism can affect sperm and health of offspring
Subject males to dietary stress, metabolic effects,even when mated to control female = risk increases of offspring with metabolic disease
You are studying inheritance of a disease phenotype (in mice) caused by chemical exposure. You this suspect this is due to increased DNA methylation at about 20 CpG islands. How could you provide experimental evidence that this was epigenetic rather than genetic inheritance? - ideas
NGs then mix with control and see
In diseased ones = should see methylation
Could do ngs on all and see no genetic genes
Look at inheritance pattern and if environmental effect =would not expect to see change, should not see reg inheritance pattern
Does the phenotype segregate with DNA methylation and not with a mutation?
Bisulfite sequencing of cpg islands = presence of methylation should strongly correlate with disease phenotype, get info about methylation
Could you rule out underlying genetic cause= ngs maybes
Should not show inheritance in families = if environmental = shouldn’t be in relatives, individual, - not regular pattern, rapid onset, nothing before
Describe mechanisms for transgenerational effects transmitted through male germ line - name 3
Dna meth
Hsitone mods
Small RNAs
Describe mechanisms for transgenerational effects transmitted through male germ line - describe dna meth
Seen in mouse, plants
Unlikely because of epigenetic reprogramming in germline, also very few changes in dna meth seen in sperm in these experiments
Hard to see it being the main mechanism, globally removed
V Describe mechanisms for transgenerational effects transmitted through male germ line - describe hsitone mods
Maybe but not very many histones retained in sperm
Males in germline.= go through dramatic changes = lose most histones, affect sperm content
Describe mechanisms for transgenerational effects transmitted through male germ line - describe small rnas
Prions? Metabolites? Hidden genetic variation? Microorganisms?
What happens to histones in sperm development
Most but not all histones are removed and replaced with protamines in late stages of dev
Som retained tho, not very robust system
Protamines do not carry epigenetic info
= epigenetic info wiped out
Describe small rnas and epigenetics
Non coding rna, processes from specific larger Aberrant transcripts that lead to double stranded dna = processed to produce small RNAs that can interfere with transcription of mRNAs, not translation, also used to produce micro RNAs
Can go back into nucleus and regulate transcription
= usually involved in. Regulating transposon - silencing them in germline
What are small rnas
22-24 nucleotide RNAs that mainly play roles in post transcriptional gene silencing
DeSCRIBE piRNAs
Germline specific version of siRNAs involved in silencing trasnposons in germline
Whaat have model organisms revealed about small RNAs
Roels for small RNAs in transcriptional silencing and epigenetic inheritance
Small RNAs =Tightly linked to epigenetic chromatin states
Not so much in mammals
Describe role of small RNAs in fission yeast
Needs specific type, needs small RNAs to form heterochromatin
Descrie role of small RNAs in nematode, c elegans
Small RNAs associated with forming heterochromatin states and form states that are transmitted through generations
Worms can transmit all kinds of environmental effects through gens
What do small RNAs regulate
Gene expression at transcriptional and post transcriptional levels
Are small RNAs transmissible between cells
Yessss
Are transmissible between cells
Could explain how a somatic exposure effects germline- can get them into sperm
Do small RNAs affect transcription
Nooooo, not in mammals
And piRNAs only known to act on highly repetitive sequences (consistent with their role genome defense from transposons)
What could be another role of other types of non coding RNAs
Maybe other types of non coding RNAs could play analogous roles at endogenous genes udner some circumstances - that lead to heritable gene expression states
