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(2)TheroleofEpigeneticInheritance

• LamarckRevisited

• Lamarckwasincorrectinthinkingthattheinheritanceofacquiredcharactersisthemainmechanismofevolution(NaturalSelectionmorecommon)

• However,wenowknowthattheinheritanceofacquiredcharactersdoeshappensometimes,throughtheinheritance ofepigeneticmodifications

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EpigeneticInheritance

HistoricalperspectiveEpigenetics:termcoinedbyC.H.Waddingtonin1942.Alterationsingeneexpression,butwheretheDNAitselfremainsunchanged.

Epigeneticmodificationshavebeenwidelyknownsincethe1970s.Notmuchintextbook,butwatch13minuteNOVAcliponepigenetics:http://www.pbs.org/wgbh/nova/body/epigenetics.html

Epigeneticinheritance:However,thatepigeneticmodificationscouldsometimesbeinherited isaveryrecentdiscovery

Westilldonotknowhowwidespreadtransgenerational epigeneticinheritanceisinanyorganism

Epigenetic Modifications• “Epigeneticmarks”(methylation,etc.)aremadeacrossthe

genomeateachgenerationtodefinecelltypesandpatternsofgeneexpressioninthedevelopingembryo.These“marks”definewhichgenesareturnedonandoff.

• Marksfromthepreviousgenerationaretypicallyremovedinthegermline,toenabletotipotency ofcellsinearlyembryos

• Epigeneticchangescouldbeenvironmentallyinduced

• Occasionallythereprogrammingisbypassedandsomeepigeneticmarksgetpassedonà LamarckianEvolution

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EpigeneticInheritance

EpigeneticInheritance:Alterationsingeneexpressionthatarepassedontothenextgeneration,butwheretheDNAitselfremainsunchanged

NOVAcliponepigenetics ifyouwantmorebackground:http://www.pbs.org/wgbh/nova/body/epigenetics.html

DNAmethylation istypicallyremovedduringzygoteformationandre-establishedthroughsuccessivecelldivisionsduringdevelopment.

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Implications:

EpigeneticEffects: Thesamegenomecouldexpressdifferentphenotypes:Epigeneticdifferencescouldresultinphenotypicdifferencesevenamongidenticaltwins(clones)

EpigeneticInheritance: Reallyrapidevolutioncouldtakeplacewithoutchangesinthegeneticcode

Outline(1)ClarificationofConcepts

(2)EpigeneticModifications

(3)EpigeneticInheritance

(4)ExampleofEpigeneticInheritance

• Epigeneticeffects:typicallynotheritablechangesingeneexpressionorcellularphenotypecausedbymechanismsotherthanchangesintheunderlyingDNAsequence.Examples:DNAmethylationandhistonedeacetylation,bothofwhichservetosuppressgeneexpressionwithoutalteringthesequenceofthesilencedgenes

• Transgenerational epigeneticeffects:Theseareregardedaseffectsonthephenotype(oronpatternsofgeneexpression)thataredetectedacrossmorethanonegenerationandthatcannotbeexplainedbyMendelian genetics(orchangestotheprimaryDNAsequence).Example:transgenerational plasticity,maternaleffects.

• Transgenerational epigeneticinheritance:Thistermreferstoeffectsonphenotype(oronpatternsofgeneexpression)thatarepassedfromonegenerationtothenextbymoleculesinthegermcells andthatcannotbeexplainedbyMendelian genetics(orbychangestotheprimaryDNAsequence).

(1)ClarificationofConcepts

IfEpigeneticModifications occuralone,theyareNOTasignofEpigeneticInheritance

ThechangesthatMATTERforevolution,whethertheyareepigeneticorgenetic(mutations),arethosethatgetpassedontothenextgenerationthroughthegermline (eggsorsperm)

Epigeneticmodificationsthatoccurinasinglegenerationareonetypeofphenotypicplasticity

EpigeneticModification(Effect)versus EpigeneticInheritance

Definition• Differencesinphenotypethatagenotypeexhibitsacrossarangeofenvironments,becauseofchangesingeneexpression

• Changesingeneexpressioncouldbecausebyenvironmentalcuesinstigatingsignaltransduction...changesingeneexpressioncouldalsobecausedbyepigeneticmodifications

• Sometraitswithaplasticcomponent:intelligence,height,temperaturetolerance,salinitytolerance,musclemass…

PhenotypicPlasticity Acclimation (≠ Adaptation)

1) Result of Phenotypic Plasticity

2) Not heritable (Not inherited)

3) Short term or developmental response within a single generation

4) Arises through differential gene expression or other regulatory mechanism rather than natural selection

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HebertandGrewe,1985

Predator induced formation of helmets in

Daphnia

Exampleofphenotypicplasticity,causedbyenvironmentalchange(notnecessarilyepigenetic)

(2)EpigeneticModifications

SomeTypesofEpigeneticmodifications(incompletelist)

• ChromatinModification: epigeneticalterationofchromatinstructure,affectinggeneexpression

Examples:MethylationHistone Modifications(acetylation,deacetylation)ChromatinRemodelling

• RNA-mediatedModifications: post-transcriptionalRNAmodifications

Examples:RNAinterference(RNAi)basedmechanism - RNAstrandsinterferewiththetranscriptionofDNAortranslationofmRNA

-- OftensmallRNAs,oftenthosethattargettransposableelements-- Seemstooccurmainlyatretrotransposons andotherrepeatedelements.

-- Genomicimprinting: wheremethylation andhistone modificationsaltergeneexpressionwithoutalteringthegeneticsequence.Wheninherited,these“epigeneticmarks”areestablishedinthegermlineandaremaintainedthroughoutallsomaticcellsofanorganism.

-- GeneSilencing:couldoccurthroughseveralmechanisms,suchashistonemodification,mRNAdestruction,orRNAinterference(RNAi).

-- Paramutation:whereinteractionbetweentwoallelesatasinglelocus,resultsinaheritablechangeinexpressionofoneallelethatisinducedbytheotherallele.Mechanismisnotfullyunderstood,butcouldoccurviamethylation orregulatoryRNAs.Paramutation violatesMendel’sfirstlaw,whichstatesthateachalleleremainscompletelyuninfluencedbytheother.

ConsequencesofEpigeneticModifications:ChangesinGeneExpression

Paramutations werefirstdiscoveredandstudiedinmaize(Zea mays)byR.A.BrinkattheUniversityofWisconsin–Madison(DeptofGenetics)inthe1950s

OriginalArticle:R.A.BrayandR.A.Brink.1966.MutationandParamutation attheRLocusinMaize.Genetics.54:137–149.

ChromatinModification

Portela &Esteller.2010.Epigeneticmodificationsandhumandisease.NatureBiotechnology 28:1057–1068

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DNA Methylation: methyl groups are enzymatically added and removed, through the action of methylases and demethylases.

The level of methylation generally correlates with the transcriptional state of a gene: active genes are less methylated than inactive genes

Examples:

Epigenetic Modifications DNAMethylationEpigeneticmodifications

DNAmethyltransferases

• Additionofamethylgroup(CH3)atthe5positionofcytosineàreducegeneexpression

• Inadultsomatictissues,methylation usuallyoccursintheCpG islands,aCGrichregion,upstreamofthepromoterregion.

• Inembryonicstemcellsnon-CpGmethylation isprevalent(significantcytosine-5methylationatCpA andCpT;Ramsahoye2000).

Methyl groups are enzymatically added and removed to DNA, through the action of methylases and demethylases.

The level of methylation generally correlates with the transcriptional state of a gene: active genes are less methylated than inactive genes

Example of a type of Epigenetic Modification:

DNA Methylation

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DNAMethylationEpigeneticmodifications

DNAmethylation iscarriedoutbyagroupofenzymescalledDNAmethyltransferases.

TheseenzymesnotonlydeterminetheDNAmethylation patternsduringtheearlydevelopment,butarealsoresponsibleforcopyingthesepatternstothestrandsgeneratedfromDNAreplication.

DNAmethyltransferases

DNAMethylation• Crucialpartofnormalorganismaldevelopmentandcellulardifferentiationinhigherorganisms

• Altersgeneexpressionpatternincells• Suppressesexpressionofviralgenesandotherdeleteriouselementsthathavebeenincorporatedintothegenomeofthehostovertime

• Playsacrucialroleinthedevelopmentofnearlyalltypesofcancer(hypermethylation,whichrepressestranscriptionofthepromoterregionsoftumorsuppressorgenes)

• Mightbethemechanismforlearningandlongtermmemorystorage

Epigeneticmodifications One way in which DNA Methylation suppresses gene expression

• Methylation atthepromotersiteorupstreamofthepromoter

• Methylation ofnucleotidesinaregulatoryelement,suchasthepromoter, orupstreamofthepromoter,couldleadtochangesingeneexpression.

• Usually,suppressionofexpressionoccursduetointerferencewithbindingofthetranscriptionfactor.

• Typicallymoremethylation leadstogreatersuppressionofgeneexpression

transcriptionfactor

changeingeneexpression

genepromoter

genepromoter

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FactorsthatcouldaffectDNAMethylation

TheEnvironment:suchasdiettoxins,vitamins,stress,affection(licking,hugging),etc.etc…

• ExampleofDNAMethylation:DNAmethylationoftheagoutigeneinmicehavebeenfoundtocausebrownskinnymice…demethylation ofthisgene(increasedexpressionofagouti)resultsinyellowfatmice

• TheAgoutiviableyellow(Avy)alleleiscreatedbyaretrotransposon insertionofanelement(intracisternal Aparticle,IAP)upstreamoftheagoutilocus.

• DNAmethylation oftheIAPpromoteratAvy reducestranscriptionoftheAvy gene(getbrownskinnymice)

DNAMethylation:Childhoodtrauma

• EarlychildhoodtraumacanleadtoDNAdemethylation oftheFKBP5geneinhumanindividualsthatpossessparticularallelesatthisgene.

• FKBP5regulatesglucocorticoid receptoractivityandstressresponse.Demethylation ofthe“AA”genotypeleadstoexcessiveglucocorticoid receptoractivation.

• Thosehomozygousforthe“A”alleleoftheFKBP5geneweremorelikelytosufferfromdepression,post-traumaticstressdisorder,oranxietydisordersinadulthood,iftheywereabusedaschildren(causingdemethylation atthislocus).

http://usrexp-sandbox.nature.com/neuro/journal/v16/n1/full/nn.3275.htmlKlengel,T.etal.Allele-specificFKBP5 DNAdemethylation mediatesgene–childhoodtraumainteractions.NatureNeurosci.2Dec2012

Histone Modifications Histone Deacetylases/Histone Acetyltransferase

• Theabilityofaparticulartranscriptionfactortobindtoitstargetgeneis,inpart,dependentonmodificationsthataremadetothehistone proteins

• AbnormalactivityofHDACs hasbeenobservedinacutepromyelocytic leukemia,acutemyelogenous leukemia,non-Hodgkinlymphoma,andsometypesofcolorectalandgastriccarcinoma

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Histone Deacetylases/Histone Acetyltransferase

Histone Acetylation orDeacetylation:affectslevelofrelaxationofthechromatinandlevelofgenetranscription.

• Histone acetyltransferases (HATs): Acetylate Histones,enhancetranscription; acetylation neutralizespositivechargesonthehistone bychangingaminesintoamidesanddecreasestheabilityofthehistones tobindtoDNA,allowinggeneexpression

• Histone Deacetylases (HDACs): Deactylate Histones, represstranscription;removeacetylgroupsfromanε-N-acetyllysineaminoacidonahistone

Exampleofhistone deacetylase:Aging

• Sirtuin orSir2proteins areaclassofproteinsthatpossesseitherhistonedeacetylase ormono-ribosyltransferaseactivity.

• AsHistone Deacetylases,Sirtuins regulatetranscription• Sirtuins havebeenimplicatedininfluencingaging,stress

resistance,insulinsignalingandmetabolism(energyefficiency),andapoptosisandcancersuppression

• Caloricrestrictionà activatesirtuinsà slowdownaging• Drugsthatactivatesirtuins mightalsoslowdownaging

• Forexample,cooperateswithHIC1toregulateactivityofp53(tumorsuppressorgene)andapoptosis

SIRT1regulatesmanyfunctionsinvolvingapoptosisandcellsurvival

DNAMethylationandHistoneDeacetylation:Goodparenting(transgenerational epigeneticeffect)

• Increasedmaternalcareresultsintwotypesofepigeneticchanges:(1) acetylation ofhistones H3-K9,and(2) demethylationofthetranscriptionfactor(NGFI-A)bindingsitetothepromoteroftheglucocorticoid receptorà higherGRactivity

• Offspringthatreceivedhighlevelsoflicking/groomingshowlowerstressresponse(happyandcalm)andbecomegoodmothersthatlicktheirpupsalot…leadingtothesameepigeneticpatterns

• Thus,thebehavioroflickingresultsinthesameepigeneticpatternbeingpassedon

Inrats,mothersthatengageinhighorlowamountsoflicking/groomingoftheirpups

http://blogs.bu.edu/ombs/2010/11/11/licking-rat-pups-the-genetics-of-nurture/http://www.nature.com/neuro/journal/v7/n8/abs/nn1276.html

• Thisisanimportantexampletoillustratethedifferencebetweenatransgenerational epigeneticeffectversustransgenerational epigeneticinheritance

• Thisisatransgenerational epigeneticeffect(maternaleffect),butNOTtransgenerational epigeneticinheritance

• ***Thisis NOTEpigenetic Inheritance becausethebehaviorispassedon,ratherthantheepigeneticmarkitself...theepigeneticmarkisinducedbythebehavioroflickingateachgeneration

DNAMethylation andHistoneDeacetylation:Goodparenting (3)EpigeneticInheritance

• Onlythoseepigeneticmodificationsthatareheritableviathegametes(germline)à leadtoepigeneticinheritance.

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(3)EpigeneticInheritance• Mostepigeneticmodifications,i.e.epigeneticmarks,thatareestablishedinmosttissuesduringanorganism’slifetimeareirrelevantwithrespecttothenextgeneration.

«Thisisbecauseepigeneticmodificationsarenormallyerasedateachgeneration.Forexample,DNAmethylation istypicallyremoved(orpossiblyoxidized;Iqbal etal.2011)duringzygoteformationandre-establishedthroughsuccessivecelldivisionsduringdevelopment.

«Andalsobecauseonlyepigeneticmodificationsofthematuregametes(andnotinothertissues)havethepotentialtocontributetothephenotypeoftheoffspring,thenextgeneration.

• Onlythoseepigeneticmodificationsthatareheritableviathegametes(germline)à leadtoepigeneticinheritance.

EpigeneticInheritance

Alterationsingeneexpressionthatarepassedontothenextgeneration,butwheretheDNAitselfremainsunchanged

Stillanewfrontier(thisfieldisstillextremelynew),withmanyexamplesinplantsandfewerconcreteexamplesinanimals

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InthetoadflaxLinaria vulgaris,radially symmetricflowers,ratherthanthetypicalbilaterallysymmetricones,iscausedbyDNAmethylation oftheCYCLOIDEAgene,whichcontrolstheformationofdorsalpetals.

ExamplesofEpigeneticInheritance

FlowerSymmetry

• Sometomatoesdonotripenandremaingreen.

• Thesetomatoeshaveaheritablecytosinehypermethylation oftheCnr genepromoter,whichinhibitsexpressionoftheCnr gene

http://usrexp-sandbox.nature.com/nbt/journal/v31/n2/full/nbt.2497.html

ExamplesofEpigeneticInheritance

EpigeneticTriggerfortomatoripening

Hypermethylation oftheCnr promoterresultsininhibitionofRINtranscriptionfactorbinding,preventingCnr geneexpressionandfruitripening.

http://usrexp-sandbox.nature.com/nbt/journal/v31/n2/full/nbt.2497.html

• MethylationatFKBP5 geneinHolocaustsurvivorsandtheiroffspring.Thisgeneaffectsglucocorticoidresponse(stressresponse),andislinkedtoPTSDanddepression(RachelYehudaetal.2015)à needsmorestudy

• Resultsarenotclearlyinterpretable(http://blogs.plos.org/biologue/2015/07/07/human-disease-epigenomics-2-0/)

• Miceexposedtotoxinspassonfearoftheodorofthattoxinontotheiroffspring(not100%conclusive)

• ExamplesofEpigeneticInheritance aremuchmorecommoninplantsandmoreconclusive

PotentialExamplesofEpigeneticInheritance(notconclusive)

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http://www.scientificamerican.com/article/descendants-of-holocaust-survivors-have-altered-stress-hormones/

http://www.nature.com/news/searching-chromosomes-for-the-legacy-of-trauma-1.15369

http://www.biologicalpsychiatryjournal.com/article/S0006-3223%2815%2900652-6/abstract

References

http://www.nature.com/news/fearful-memories-haunt-mouse-descendants-1.14272

http://usrexp-sandbox.nature.com/nbt/journal/v31/n2/full/nbt.2497.html

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Whichchangesallelesfrequencies?Whichchangesgenotypefrequencies?

• Selection• GeneticDrift• Inbreeding• Recombination• Mutations• Migration(Geneflow)• Epigeneticmodifications