Plant responses to abiotic stress: The chromatin context of transcriptional regulation

17 Pages·2016·0.92 MB·English

BiochimicaetBiophysicaActa1860(2017)106–122
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Biochimica et Biophysica Acta
journal homepage: www.elsevier.com/locate/bbagrm
Review
Plant responses to abiotic stress: The chromatin context of
transcriptional regulation
⁎
María-AmparoAsensi-Fabado,AnnaAmtmann,GiorgioPerrella
PlantScienceGroup,MCSB,MVLS,UniversityofGlasgow,Glasgow,G128QQ,UK
a r t i c l e i n f o a b s t r a c t
Articlehistory: Theabilityofplantstocopewithabioticenvironmentalstressessuchasdrought,salinity,heat,coldorflooding
Received9May2016 reliesonflexiblemechanismsforre-programminggeneexpression.Overrecentyearsithasbecomeapparent
Receivedinrevisedform9July2016 thattranscriptionalregulationneedstobeunderstoodwithinitsstructuralcontext.Chromatin,theassembly
Accepted26July2016
ofDNAwithhistoneproteins,generatesalocalhigher-orderstructurethatimpactsontheaccessibilityandeffec-
Availableonline31July2016
tivenessofthetranscriptionalmachinery,aswellasprovidingahubformultipleproteininteractions.Several
studieshaveshownthatchromatinfeaturessuchashistonevariantsandpost-translationalhistonemodifications
Keywords:
arealteredbyenvironmentalstress,andtheycouldthereforebeprimarystresstargetsthatinitiatetranscription-
Co-expression
Functionalgenomics alstressresponses.Alternatively,theycouldactdownstreamofstress-inducedtranscriptionfactorsasanintegral
Agriculture partoftranscriptionalactivity.Afewexperimentalstudieshaveaddressedthis‘chicken-and-egg’problemin
Crops plantsandothersystems,buttodatethecausalrelationshipbetweendynamicchromatinchangesandtranscrip-
Networkanalysis tionalresponsesunderstressisstillunclear.Inthisreviewwehavecollatedtheexistinginformationonconcur-
Guilt-by-association rentepigeneticandtranscriptionalresponsesofplantstoabioticstress,andwehaveassessedtheevidenceusing
asimpletheoreticalframeworkofcausalityscenarios.
ThisarticleispartofaSpecialIssueentitled:PlantGeneRegulatoryMechanismsandNetworks,editedbyDr.
ErichGrotewoldandDr.NathanSpringer.
©2016TheAuthors.PublishedbyElsevierB.V.ThisisanopenaccessarticleundertheCCBYlicense
(http://creativecommons.org/licenses/by/4.0/).
1.Introduction absenceofacentralbrain,theregulatorycircuitsthatgenerateadaptive
responsesinplantsdifferconsiderablyfromthoseinanimals[3].What
Plantsexperienceaneverchangingenvironment,rangingfromfast iscommontoadaptiveresponsesinalllifeformsisthattheydependto
fluctuationsoflightandhumiditycausedbyclouds,windorrain,to alargeextentondynamicchangesingeneexpression.
largerdiurnalandseasonalchangesintemperature,light,rainfalland Transcriptionalresponsesofplantstoenvironmentalstressfactors
nutrientavailability.Insomeenvironmentsplantshavetodealwith have been investigated extensively over the last decades, from
extremeconditionsofpermanentorfrequentnature,whereasinother genome-widetranscriptprofilingundermultiplestresscombinations
environmentsseriousstressonlyoccurssporadically andtherefore totheunravellingofspecificsignallingpathwaysandtheidentification
doesnotprovideevolutionarypressureforpermanentadaptations. ofindividualregulatoryproteinsandtheirtargets.Theresearchhas
Neverthelessplantsneedtohaveasafetynetinplacetodealwith generatedalargebodyofdetailedinformationonhowplantsrespond
occasional stress events. Flexibility is an essential requirement for to abiotic stresses such as cold, heat, drought, salinity or flooding
survivingstressatasedentarylifestyle.Plantsmaintainthisflexibility [4–9].Theknowledgegainedhasalreadybeenusedtoimprovecropre-
byoperatingasignal-responsenetworkthatallowsthemtorapidly silience, e.g. through stress-inducible up-regulation of transgenes
re-programmetheirdevelopment,physiologyandmetabolisminre- encodingenzymesthatproducestressprotectantsortheirregulators
sponsetoenvironmentalstress[1,2].Theabilityofplantstoperceive [10].Overrecentyearsscientistshavebecomeincreasinglyawareof
andintegrateanenormousamountofenvironmentalinformationand the fact that transcriptional regulation cannot be fully understood
torespondtoanygivensituationinanadhocmannerhasoftenledto unlessweconsiderthestructuralcontextinwhichitoccurs.DNAisas-
comparisonswithintelligentbehaviourofanimals,althoughinthe sembledwithhistoneproteinstoformchromatin,whichenablesa
higherorderstructure.Chromatinprovidesameanstostabiliseand
condenseDNAbutitismuchmorethanapackagingdevice;itisdynam-
⁎ Correspondingauthorat:PlantScienceGroup,InstituteofMolecular,CellandSystems
ic and can be altered by developmental or environmental stimuli
Biology(MCSB),CollegeofMedical,VeterinaryandLifeSciences(MVLS),Universityof
Glasgow,GlasgowG128QQ,UK [11–16].Itisoftenassumedthatenvironmentallyinducedchangesin
E-mailaddress:[email protected](G.Perrella). chromatinstatuscontrol,oratleastmodify,transcriptionalresponses
http://dx.doi.org/10.1016/j.bbagrm.2016.07.015
1874-9399/©2016TheAuthors.PublishedbyElsevierB.V.ThisisanopenaccessarticleundertheCCBYlicense(http://creativecommons.org/licenses/by/4.0/).
M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122 107
butthisnotionisstillbuiltonrelativelyspareevidence.Inthisreview thestress-inducedgenes[45].Furthermore,someDNA-demethylases
wehavetriedtocollateandtoassesstheexistinginformationthat targetTE sequences within thepromoters ofstress-regulatedgenes
linksepigeneticprocesseswithtranscriptionalresponsesofplantsto [46].Thequestionwhetherstress-inducedchangesinDNA-methylation
abioticstress. statuscouldbeheritableandgenerateatrans-generationalmemoryof
stressexperiencehasbeenamatterofintenseresearch,butremains
1.1.Chromatinstructure–settingthescene controversial.Inordertoprogressintothenextgenerationstress-
inducedchangesofDNA-methylation status wouldneedto ‘slip’
DNA iswrappedaroundproteinunitscallednucleosomes.Each throughaveryeffectiveresettingprocessinthegermline[47–49].
nucleosomeisanoctamercomposedoftwocopiesofhistonesH2A, Inheritanceofre-activatedTEsortransgenesintothenextgenera-
H2B,H3,andH4,whichassociateswithapproximately146bpofDNA tionisthereforeaveryrareevent,althoughitcanbeobservedinmu-
[17].H1isassociatedwiththelinkerDNAbetweennucleosomes(30– tants with defects in the processes underpinning resetting, for
100bp),andcauses further compaction [18,19].Whilethis overall examplethegenerationofsiRNAs[50–52].Importantly,however,if
arrangement is ubiquitous its exact composition and structure can changes in DNA-methylation patterns are artificially introduced,
change,bothlocallyandtemporally[20].Thechromatinstatusdeter- e.g.throughmutationsingenesthatmaintainDNA-methylation,
minestheaccessibilityandeffectivenessofthetranscriptionalmachin- thesecanbeinheritedovermanygenerations,eveniftheoriginal
ery(polymerasesandregulatoryproteins),andthereforechromatin mutantalleleisoutcrossed.Thishasallowedthegenerationofstable
remodellingisapotentialmeanstocontrolgeneexpression.Thebasic epi-RILsandnewphenotypicvariation[53,54].
molecularprocessesunderpinningchromatindynamicsare(1)the Thevastmajorityoftranscriptionalresponsestoenvironmental
exchangeofhistonevariants,(2)DNA-methylationand(3)histone stresswilloccuroutsidetheheterochromaticregionsinthetranscrip-
modifications.Thefactthattheseprocessesimpactongeneexpression, tionallycompetenteuchromatin,whichharboursmostgenes(Fig.1).
andhenceonthephenotypeofaplant,withoutalteringthegenetic EuchromatinhasgenerallyalowlevelofDNAmethylation,although
code,hasledtotheirgeneralassociationwiththeterm‘epigenetics’,al- CGDNAmethylationoccurswithingenebodiesof13.5%Arabidopsis
thoughsomescientistsarguethatthistermshouldbereservedtoheri- genes,andmightbeanimportantfeatureofhighlyexpressed,constitu-
tablephenomena. tivelyactivegenes[55,56].
1.1.1.Histonevariants 1.1.3.Histonemodifications
Eachhistonetypeisrepresentedbyanumberofvariantswithsmall Euchromatinislesscompactthanheterochromatinandaccessibleto
differencesinaminoacidsequenceandstructure.Histonevariantsdiffer thetranscriptionalmachineryincludingpolymerasesandtranscription
intheiraffinityforDNAandforhistonebindingproteins,andtherefore factors.Itisthereforeprimarilyatthislevelofchromatinorganisation
replacementofonehistonevariantbyanothercouldaltercompaction that short-term regulation of gene expression occurs. Signalling
statusandrecruitmentofregulatoryproteincomplexes.TheH3variants pathwaysinvolvingplanthormonessuchasabscisicacid(ABA),ethyl-
H3.1andH3.3ofArabidopsisdifferonlyinfouraminoacids[21],yetthey ene, jasmonate or brassinosteroids, connect environmental stress
areassociatedwithdifferentpartsofthegenome[22].WhileH3.1cor- perceptionwithactivationoftranscriptionfactors,whichinturnbind
relateswithsilencedgenomicregions,H3.3preferentiallyoccursinre- tothepromoterregionsoftheirtargetgenesandeitherinduceorre-
gions of active gene transcription and rapid nucleosome turnover pressthem.Thisprocessoccurswithinthelocalchromatincontext,
[23–25].ReplacementofH3.1byH3.3accompaniesimportantprocess- whichpotentiallyprovidesanadditionallevelofcontrol.
essuchasdevelopmentalre-reprogramming[26].Similarly,theH2A The important dynamic features of euchromatin are post-
variantH2AZreplacesH2AXingenomeregionswithactivetranscrip- translational modifications of the histones. The so-called ‘histone
tion[27].AnotherH2Avariant,H2AW,functionsinthesilencingofhet- code’iscomplex[57,58];itincludesarangeofchemicalmodifications
erochromaticsequences[28,29].TheArabidopsisgenomealsocontains (methylation,acetylation,phosphorylation,ubiquitination)ofdifferent
threegenesencodingvariantsofthelinkerhistoneH1[30].H1.1and residues(mostlylysinesandargininesintheN-terminalhistonetails)
H1.2aremostlikelyproductsofgeneduplicationandexistinastable atvariouslevels(e.g.mono-,di-andtri-methylation)andinmultiple
pooloccupyingpreferentiallyheterochromaticregions.Bycontrast, combinations (e.g. the same residue can be both methylated and
H1.3ismoredivergentandhasafasterturnover;itshowsspecificex- phosphorylated) [59–64]. In this review we will employ the usual
pressioninguardcells,andcanbeinducedinothertissuesbyabiotic terminologytolabelhistonemodifications,e.g.H3K4me3standingfor
stress[31–35].Stress-dependentdepositionofhistonevariantspro- histoneH3tri-methylatedinlysine4.Considerableefforthasbeen
videsapotentialmeanstolinkenvironmentalsignalstodownstream made to monitor histone modifications in individual genes and
transcriptionalresponses.Currentevidencesupportingthisparadigm genome-wide,andtocorrelatethemwitheachotherandwithdown-
willbereviewedbelow. stream processes such as transcription, DNA repair and chromatin
condensation.Therefore,themajorityofstudiesinvestigatingchroma-
1.1.2.DNA-methylation tin processes in relation to transcriptional stress responses have
DNA-methylation(5-methylcytosineinvarioussequencecontexts) focussedonhistonemodifications.Beforedescribingthesestudiesin
isparticularlyprominentinthecentromericandpericentromericre- more detail, we will discuss possible causal relationships between
gions of the chromosomes that are rich in transposable elements signals,chromatin,transcriptionandresponsesinordertoestablisha
(TEs).AccumulationofDNA-methylationinallcytosinecontextsresults conceptualframeworkforassessing andinterpretingtheempirical
inhighlycondensedchromatin(heterochromatin),whichprevents evidence.
transcriptiontherebysilencingTEs[36,37].Themechanismofsilencing
throughDNA-methylation,involvingsmallRNAsandhistonemodifica- 1.2.Chromatinmodificationsandtranscription-causalscenarios
tionssuchasH3K9me2hasbeeninvestigatedingreatdetailandis
reviewedelsewhere[38–42].Removaloflinkerhistonesseemstobere- Consideringtheimportanceofchromatinstructurefortranscrip-
quiredtoallowaccessfortheDNA-methylationmachinery[30,43]. tionalcompetenceandtranscriptionalregulationitisclearthatchanges
In the laboratory, certain stress treatments, e.g. prolonged or inthisstructurewillhaveeffectsonprocessesthatrequiretranscrip-
repeatedhightemperature,canreleasesilencingoftransgenesorTEs, tionalre-programming.Itisthereforenotsurprisingthatmutantsthat
andinsomecaseofneighbouringgenes[44].Viceversa,transcriptional areimpairedincrucialprocessesunderpinningchromatinstructure
regulation in response to low-phosphate stress of rice has been willbeaffectedindevelopmentaltransitions,suchasgerminationand
reportedtocausetransienthypermethylationofTEsinthevicinityof flowering,orinresponsestoenvironmentalstresses.However,the
108 M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122
Heterochromatin
Silencing
Euchromatin
(DNA-methylation,
sRNAs, histone variants)
Histone Induced
Transcriptional
modifications
regulation
(transcription factors,
enhancers, repressors,
chromatin remodelingcomplexes) Repressed
Abiotic
Stress
Fig.1.Levelsofgeneexpressioncontrolinthechromatin.Chromatin,theassociationofDNA(blackline)withnucleosomesmadefromhistoneproteins(paleblue),facilitatestight
packagingofthegeneticmaterialinchromosomes.Chromatinstructuredetermineswhetherornotageneistranscribedandatwhatrate.Geneticinformationinthehighly
condensedheterochromatinissilenced.Genesinthelesscondensedeuchromatinaretranscriptionallycompetent,‘poised’tobetranscribedbyRNA-polymerases.Transcriptionfactors
andotherregulatoryproteins(multiplecolours)thatbindtotheupstreampromoterregions(triangles)canactivate(induce)orinhibit(repress)geneexpression.Multi-protein
complexescontaininghistone-modifyingenzymesalsoassociatewiththeDNAtoattachorremovechemicalmodificationsonhistonetails(differentlycolouredextrusionsfromthe
nucleosomes).Chromatin-remodellingcomplexesalsoassociatewiththechromatintoexchangehistonevariantsand/oralternucleosomespacing.Howabioticstresssignalsregulate
geneexpressionwithinthechromatincontextisatopicofactiveresearch.
fact that a particular chromatin-modifying enzyme is required for histonemodificationswithinthegenesequence,butthisremainsto
transcriptionalchangesdoesnotnecessarilymeanthatitisactivelyin- beproven.Secondly,thecurvesareonlylinearinthelowerpart.They
volvedinbringingaboutsuchchanges.Forexample,ifproductionofa flatten withincreasingvaluesfortranscript levels,indicatingweak
compatibleosmolyterequirestranscriptionofabiosyntheticenzyme, correlationforgeneswithmoderateorhighexpressionlevels.Thus
itispossiblethatknockoutofadeacetylase,whichrepressesthepartic- up-regulationofagenethatisalreadyhighlyexpressedisunlikelyto
ulargeneleadstoenhancedosmoticstresstoleranceofthemutant. beaccompaniedbyachangeinhistonemodification,andviceversa.
However,wecannotconcludethattheplantusesasimilartacticduring Evenmoreimportantinthecontextofstress-inducedresponses,isthe
regulation.Toascertainthelatterwewouldneedtomeasureachange factthatthecorrelationswereestablishedundersteady-statecondi-
in the histone acetylation status of thegene and link it causally to tions.Thereisnoreasonwhythecorrelationsshouldnolongerhold
both,theupstreamregulationofthedeacetylasebytheenvironmental oncetheplanthasadaptedtoalong-termconditionthatdiffersfrom
stimulusandthedownstreamregulationofthegeneinquestion.To thecontrol,e.g.lowerwateravailabilityorhighertemperature.Itis
datemanystudieshavereportedstress-tolerant/sensitivephenotypes thereforenotsurprisingthatstudiesmonitoringhistonemodifications
of mutants defective in chromatin-related genes, but establishing andtranscriptlevelsinplantsthathaveexperiencedastresscondition
causalitieshasprovenmoredifficult,especiallybecausemanymutants foraprolongedperiodoftimefindsimilarcorrelations.Thus,ifthe
have already developmental phenotypes in unstressed conditions, ‘stress-inducedchanges’aresimplydefinedasthedifferencesbetween
whichmayaffecttheirperformanceunderstress. thetwosteadystates,‘changes’inchromatinmarksand‘changes’in
Similarly,correlativeobservationsdonotproveacausalrelationship. transcriptionwillagainbecorrelated.Bycontrast,whenhistonemodi-
Thenotionof‘active’and‘repressive’marksisoftenusedtoarguethat ficationsandtranscriptlevelswererecordedimmediatelyafterthe
stress-inducedchangeinacertainhistonemodificationwillleadtoa stress treatment, e.g. over the first 24 h after salt application [30],
transcriptional change, yet this terminology is purely based on everygenetesteddifferedintheirkineticprofilesoftranscriptlevel
genome-widecorrelations.Plottinggenome-widehistonemodifica- andhistonemodification,andmostofthechangesdidnotfollowthe
tionsofchromatininArabidopsisrootsagainsttranscriptlevelsinthe patternpredictedformthesteadystatecorrelations.Clearly,atour
sametissuesconfirmedindeedapositivecorrelationbetweentranscript currentstateofknowledge,thenotionof‘active’or‘repressive’mark
levels and H3K4me3 (an ‘active’ mark) and a negative correlation isnotsufficientforidentifyingcausalrelationshipsbetweenstress-
betweentranscriptlevelsandH3K27me3(a‘repressive’mark)[65],as inducedchangesofhistonemodificationsandstress-inducedchanges
shownbeforeforothertissues.However,afewpropertiesofthecurves oftranscriptlevels.
arenotable.Firstly,inordertorevealthecorrelations,histonemodifica- Theoretically,chromatinmodificationscouldbecausallylinkedto
tionandtranscriptlevelshadtobeaveragedoverseveralhundredsof transcriptional responses in a number of ways, as schematically
genes, meaning that the relationship does not hold for individual showninFig.2.Inthefirstscenario(1)thechromatinfeaturesarenot
genes,andisthereforenotdiagnostic.Itispossiblethatcorrelationat themselvesalteredbythestressbuttheirassociationwithaparticular
single-genelevelcouldbeimprovediftheresolutionwasincreased gene before the stress may determine whether a stress-induced
withrespecttoboth,individualcelltypesandexactlocationofthe regulatory protein can exert its function or it may modulate its
M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122 109
Chromatin
modification
(1)
Regulation of
Stress signal Response
transcription
2)
Chromatin Regulation of
Stress signal Response
modification transcription
(3)
Regulation of Chromatin
Stress signal Response
transcription modification
Chromatin
(4) modification
Regulation of
Stress signal Response
transcription
Fig.2.Causalityscenariosfortheroleofchromatinmodificationsintranscriptionalstressresponses.Inthefirstscenario(1)chromatinmarksarenotthemselvesalteredbythestressbut
theirassociationwiththegenebeforethestressmaydeterminewhetherastress-inducedregulatoryproteincanexertitsfunction,ormaymodulatethestrengthoftheresponse.Inthe
secondcase(2)themarkistheprimarytargetofthestresssignalanditschangecausesdownstreamtranscriptionalregulationofthegenesassociatedwiththeparticularmark.Thethird
scenario(3)describesasituationwhereachangeofchromatinisinfactpartofthetranscriptionalregulation,actingdownstreamofastress-inducibleregulator.Forexamplea
transcriptionfactormayrecruitahistonemodifyingenzymewhichthenenhancesorrepressestranscription.Inthelastcase(4),thestressaltersboth,chromatinmarksandgene
transcription,butthetworesponsesoccurindependentlyandtheformerisnotnecessaryforthelatter.Theindividualelementsofthecausalpathwaysmayenhanceorinhibiteach
otherinfeedbackloops(e.g.(3)dottedline),andtheymayconnectonescenariotoanotherfordifferentstressesormodifications.Fordetaileddiscussionseetext.
efficiency.Anobvious,yetunprovencaseisacell-typespecificresponse alters chromatin features and transcription, but the two responses
wheretheactionofatranscriptionfactordependsonwhetherthetarget occurindependently.Toproveindependenceoneneedstoshowthat
geneistranscriptionallycompetentinthiscell-typeornot.Itissimilarly eachchangecanbeeliminatedwithoutalteringtheother.Forexample,
plausiblethatthisscenarioenablesresponsivenesstodependonthe oneshouldtestwhetherknockoutmutantsforthetranscriptionfactor
physiologicalstateoftheplantatthetimeofstressexperience.To orthehistone-modifyingenzymestillproduceastress-inducedchange
provethisscenario,itwouldbeimportanttocomparetheresponsive- inthehistonemarkorthetranscript,respectively.
nessofaparticulargeneindifferentcelltypesorphysiologicalstates, Inreality,theabovelistedexperimentalstrategiestoproveapartic-
and to relate any differences to cell-type/state specific chromatin ularcausalrelationshiparedifficultifnotimpossible,themainreason
modifications.Inthesecondscenario(2),thechromatinisinfactthe beingredundancyofgenefunctionsunderpinningchromatinmodifica-
primarytargetofthestresssignal.Changesofchromatinmodifications tionsandtranscriptionalregulation.Forexample,histone-modifying
wouldthencause(andbenecessary)fordownstreamtranscriptional enzymes are encoded by many genes with overlapping expression
regulationofthegenesassociatedwiththeparticularmark.Thisscenar- patterns.Biochemicallytheyareratherpromiscuous,obtainingtheir
ioisoftenimpliedwhenscientistsreportchangesinhistonemodifica- specificity primarily through association with other proteins that
tionprofilesuponstresstogetherwithchangesingeneexpression. guidethemtothetargethistone(histone-bindingproteins)andtothe
However,toprovethiscase,onewouldneedtopreventthechangein targetDNA(e.g.co-repressors).Similarly,histonevariantreplacement
the histone mark, for example through knockout of the respective and nucleosome re-positioning is mediated by multi-protein com-
histone-modifyingenzyme,andshowthatthetranscriptionalresponse plexes.Veryfewofthesecomplexeshavebeencharacterisedfortheir
no longer occurs. Optimally, impairment of the enzyme should be nativecompositioninplants,andtheycanbeexpectedtoaltertheir
limitedtothestresssituation,forexamplethroughRNAiunderthecon- contingentofproteinpartnersdependingoncell-type,developmental
trolofastress-induciblepromoter.Thethirdscenario(3)describesa stageandenvironment.Thus,inmostcasesthespecificinteraction
situationinwhichtheprimarytargetofthestresssignalisatranscrip- modulesofmodifiersandregulatorsthatunderpinaparticulartran-
tionfactorandachangeofchromatinpropertiesisthenpartofthetran- scriptionalresponseremaintobeidentified.
scriptionalregulation.Forexample,repressivetranscriptionfactorscan Thedistinctionintothedifferentscenariosisalsosimplistic,because
recruitco-repressorproteinsthatareintegralcomponentsofhistone theindividualcasesarelikelytobeinterrelatedbothinspaceandin
deacetylation complexes. Subsequent deacetylation of the histones time.Forexample,histone-bindingproteinsinhistonedeacetylation
associatedwiththetargetgenewouldthenrestrictaccessofthetran- complexesoftenhavereadingfunctions,meaningthattheyonlybind
scriptionalmachinery.Toprovethiscase,bindingregionsofrepressor tohistonesthathaveparticularmodifications(e.g.SHL1andING1/2
orco-repressorcouldbealtered,andthisshouldpreventthestress- specificallybindtoH3K4me3[66,67]).Arepressorcanonlyrecruitthe
dependentdown-regulationofthegene.Novelgeneeditingtechniques histonedeacetylationcomplexifthetargethistonehastheparticular
offeranopportunitytocarryoutsuchexperimentswithouttheneedto modification.Thisconnectsscenario3toscenario1wheretheaction
over-expressthemutantproteins.Inthelastscenario(4),thestress oftherepressordependsonthehistonemodificationstatuspriorto
110 M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122
thestress.Furthermore,changesofhistonemodificationsandtranscrip- foundtobelesssensitivetotemperaturechanges[70].Whengrown
tion are likely to differ in their dynamics [30]. Histone marks are at cool temperatures (12–17 °C) the mutant plants pheno-copied
relativelystableandcanbetransmittedthroughmitosis,theytherefore wildtypeplantsgrownat27°Candtheydisplayedaconstitutivehigh-
canoutlasttranscriptionalactivity.Thissituationcouldlinktheoutcome temperaturetranscriptome.Agenome-wideanalysisofH2A.Zandtran-
ofscenarios2or3toscenario1ifthestressisrepeated,therebyproviding scriptlevelsrevealedthatdepositionofH2A.Zwithingenebodiescorre-
abasisforprimingandacclimation.Withinashortertimeframe,thehis- latednotjustwithlowertranscriptlevelsbutalsowithhighvariationof
tonemodificationsoccurringinscenarios2or3couldinhibitorenhance transcriptlevelsacrosstissuesandenvironmentalconditions[56].In
transcriptionofthesamegene(cis)orofothergenes(trans).Forexample, combinationwiththereportedanti-correlationbetweenH2A.Zand
negativefeedbackinciscouldbeameanstogeneratetransienttranscrip- DNAmethylation,thissuggeststhatgene-bodymethylationmaybea
tionalresponses,asareoftenobservedafterasuddenonsetofstress. meanstoevictH2A.Zinordertoconstitutivelymaintainhighexpres-
Despite its obvious over-simplification, a distinction of possible sionlevels.Theobviousfollow-onquestioniswhetherenvironmental
causalrelationshipsasdepictedinFig.2ishelpfulwhenassessingthe stimuli actively alter H2A.Z disposition. Comparing H2A.Z profiles
existingevidence.Inthefollowingsectionswewillreviewstudiesthat alongtemperature-responsivegenesbetweenArabidopsisplantsex-
havemonitoredchromatinmodificationsandgeneexpressionchanges posedto17°Cor27°CrevealedhigherlevelsofH2A.Zatthelowtem-
inresponsetoabioticstresstreatments,andwewilltrytosummarise perature [70]. While this indicates temperature-dependent H2A.Z
themincausalmodelsifpossible. depositiontherelationtothetranscriptionalresponseisunclearsince
theshiftinH2A.Zleveloccurredirrespectiveofwhetherthegenes
2.Experimentalevidence wereup-,down-,orunregulatedbythetemperaturechange.Intheab-
senceofaconclusivecausallinktheevidenceavailabletodatefavoursa
2.1.Stress-dependentdepositionofhistonevariants modelshowninFig.3A,inwhichtheH2A.Zstatuspriortothestressde-
terminesstressresponsivenessofindividualgenes,whichisreminis-
TheroleofH2Avariantsingenetranscriptionandstressresponses centofscenario1inFig.2.
was investigated in Arabidopsis mutants defective for H2A.Z or for H1variantsinplantsfallintotwogroups;theubiquitouslyand
componentsoftheSWR1complexthatdepositsH2A.Z[68,69].Lossof stablyexpressedmajorvariantsandstress-inducibleminorvariants.
functionofSWR1-complexcomponentsledtoreducedsensitivityto ThelatterincludeH1.3inArabidopsis,H1-C/Dintobaccoandwildtoma-
pathogens and constitutively high transcript levels of pathogen- to,andH1-Sintomato.Drought-inducibilitywasreportedinallspecies
induciblegenes[69].MutantsforH2A.ZandSWR1-proteinswerealso tested,butmutantanalysisrevealednoobviousfunctions,apartfrom
A
Gene body
Constitutive
DNA-methylation
transcription
Histone variant
replacement
H2A.X H2A.Z
High low Regulation of
Response
temperature transcription
B
Histone variant
replacement
H1.1/2 H1.3
Up-regulation
of H1.3 DNA-methylation
(CHH)
Drought Regulation of
Response
Low light transcription
Fig.3.Roleofhistonevariantsreplacementinstressresponses.A:Histone2variants:Thecombinedevidenceavailabletodatefavoursamodel,inwhichtheH2A.Zstatusdetermines
whetheragenecanbetranscriptionallyregulatedornot.H2A.Zdepositionisenhancedinthecoldandincreasestheplant'ssensitivitytothetemperaturechange.Gene-body
methylationmaybeameanstoevictH2A.Zinordertomaintainhighexpressionlevelsofconstitutivelyexpressedgenes.TheexactmolecularprocessesthatmediatebetweenH2A.Z
depositionandtranscriptionalresponsesremaintobeestablished.B:Histone1variants:ExperimentalresearchsuggestsamodelinwhichthecanonicalH1variants(H1.1,H1.2)
preventaccessoftheDNA-methylationmachinerytotheDNAundernormalconditions,butarereplacedbythemoremobile,smallerH1.3variantunderstress,therebycausingDNA
hyper-methylationinCHHcontext.TheobservationthatH1.3-mediatedDNA-methylationisshiftedtowardsexpressedgenesindicatesapotentialeffectofvariantreplacementon
geneexpression,buttheexactmechanisticlinkbetweenstress-inducedhyper-methylation,transcriptionalregulationandphysiologicalresponsesremainstobeelucidated.Fordetails
andreferencesseemaintext.
M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122 111
tomatoH1-Swhichwasshowntomaintainwaterstatusduringdrought SWI2/SNF2,isakeytargetoftheABA-dependentde-/phosphorylation
stress [71–76]. Only recently, the function of Arabidopsis H1.3 was switchoperatedbyPP2C-AandSnRKs[80,82].BRMresidesontarget
analysedinmoredetail[33].Itwasfoundthatinunstressedconditions lociofABAsignalling(e.g.ABI5)andrepressesthem.ChIPshowed
H1.3wasspecificallyexpressedinguardcells.h1.3mutantsdisplayed that BRM occupancy is independent of ABA, but phosphomimetic
decreasedstomataldensityinyoungleaves,reducedCO assimilation mutantsrevealedthatBRMneedstobede-phosphorylatedtobeactive
2
rateperplantandalteredexpressionofgeneswithknownfunctionin andtorepressthetargetgene[82].Furthermore,BRMdirectlyinteracts
guard cell development.Thesedifferences didnot impacton plant withtheclade-APP2CsHAB1andPP2CA,aswellaswiththeSnRKs
growthundernormalconditionsorunderdroughtinhighlight.Howev- 2.2,2.3and2.6/OST1[82].Thecurrentmodelisthatintheabsenceof
er,whendroughtwascombinedwithlowlighttheh1.3plantshad ABA,thePP2Csmaintainanactive,de-phosphorylatedstateofBRM
lowerleafnumberandweight[33].Indeed,H1.3wasstronglyinduced therebypreventingexpressionofABA-responsegenes.UponanABA-
inalltissuesbylowlight,withasynergisticeffecttothepreviously signal,PP2CsareremovedandBRMcanbephosphorylatedbySnRKs,
shown induction by drought. The authors also determined histone whichleadstoitsinactivationandreleasestherepressionoftheABA-
mobilitythroughFluorescenceRecoveryAfterPhotobleaching(FRAP) induciblegene[82].AssummarisedinFig.4,theevidenceobtainedso
inplantsexpressingGFP-fusionsofthedifferentH1variants[33].The farpositionsBRMbetweentheenvironmentalsignalandthetranscrip-
measurementsrevealedthatH1.3hasconsiderablyhighermobilityin tionalresponseandthereforereflectsthecausalscenario(2)inFig.2.
thechromatinthanthemainvariantsH1.1.andH1.2,suggestingthat TheexactmodebywhichBRMrepressesthetargetlociremainstobe
understressitcouldoutcompetethem.Inaccordancewiththisnotion, determined,butmayinvolvenucleosomerepositioning[80].
anincreaseofDNAmethylation(particularlyinCHHcontext)upon KnockoutbrmmutantsshareanABA-hypersensitivegermination
combined low-light/drought stress was dependent on a functional phenotypewithswi3cmutantssupportingthenotionthatSWI3Cisa
H1.3.AssummarisedinFig.3B,theevidencetodatefavoursamodel subunitofinthesamecomplex[77,83].However,theoppositepheno-
inwhichH1.1/2variantsprotecttheDNAundernormalconditions, typewasreportedforswi3bmutantsdefectiveforanotherSWI3homo-
butarereplacedbythemoremobileH1.3understress.Thisallows log[82].swi3bseedswerelesssensitivetoABAduringgerminationand
accessoftheDNAmethylationmachineryandhypermethylation.Com- showedareducedexpressionoftheABAresponsivegenes,RAB18and
parison of DNA-methylation patterns between h1-variant mutants RD29B.AsBRM,SWI3BwasalsofoundtodirectlyinteractwithHAB1
showedthatH1.3-mediatedDNA-methylationisslightlyshiftedfrom [79].OnepossibilityisthatSWI3BcompeteswithBRMforHAB1binding
TE targets towards expressed genes [33]. While this observation therebyde-phosphorylatingBRM.AnotherpossibilityisthatSWI3Bis
indicatesapotentialeffectofvariantreplacementongeneexpression, associatedwithadifferentcomplexwithdistinctfunctiontotheBRM/
theexactmechanisticlinkbetweenstress-inducedhypermethylation, SWI3Ccomplex[77,84].
transcriptionalregulationandphysiologicalresponsesremainstobe
established. 2.3.Histoneacetylationmarksandtranscriptionalregulationunderabiotic
stress
2.2.Chromatinre-modellingcomplexesasdirecttargetsofdroughtstress
signals Histoneacetylationreduceschargeinteractionsbetweenhistones
andDNAwhereasdeacetylationincreasesthem,andthesechanges
SWI/SNF-typeATP-dependentchromatinre-modellingcomplexes facilitate or impede transcription respectively [85–91]. Histone
areevolutionarilyconservedmulti-proteinmachinerieswhichcontrol acetylation/de-acetylationiscatalysedbyhistoneacetyltransferases
DNAaccessibilityandchromatinstructure[77,78].Thesecomplexes (HATs)andhistonedeacetylases(HDAs).Manyofthegenesencoding
enablehistonevariantreplacementandnucleosomere-positioning, these enzymes have been identified in plants such as Arabidopsis,
andhavealsobeenshowntoalterhistone-DNA interaction during tomato, maize, rice, barley and grapevine, as well as Brassica and
stressresponse[78–80]. Brachypodium [85,92–97].Analysis of histone modification sites by
Asuiteofstudiesinvestigatingmutantsdefectiveforproteincompo- mass spectrometry and biochemical assays [60,98] has indicated a
nentsofSWI/SNF-typecomplexesinArabidopsishaveestablisheda highconservationbetweenplantsandotherorganismsfortheposition
mechanisticlinkbetweenwaterstressandtranscriptionalresponses andthepost-translationalmodificationofindividualsites.Amongthe
throughchromatinremodelling.Underwaterstress(e.g.drought,salt) differentlysineresiduesfoundtobereversiblyacetylatedwithinthe
plantsproducethehormoneABA,whichbindstoABA-receptorsand H3andH4tails,severalhavebeenreportedtorespondtoabioticstress
enablesthemtorecruitPP2C-Aphosphatases.Thisreleasesinhibition eitheratasingle-geneoratwhole-genomelevel.Anumberofstudies
ofSnRK2-typekinases,whichinturnphosphorylateandactivateABA- thathaveinvestigatedtheeffectsofabioticstressonbothhistoneacet-
ResponseElement(ABRE)transcriptionfactors[1,81].Thereisnow ylationandtranscriptlevelsarelistedinTable1,andaresummarisedin
convincingevidencethatBRAHMA(BRM),theATPasecomponentof thefollowingtext.
ABA-inducible
genes (e.g. ABI5)
BRM
PP2C-A
Water or active Repressed
pt Post-germination
deficit, ABA e
c arrest
salt Re SnRK P -BRM De-repressed
inactive
Fig4.Roleofchromatinremodellinginstressresponses.BRAHMA(BRM),theATPaseofaSWI2/SNF2chromatinremodellingcomplexresidesonABA-regulatedlociandinhibits
transcription.BRMisadirecttargetoftheABA-perceptionmoduleandpositionsthechromatinmodificationbetweentheenvironmentalsignalandthetranscriptionalresponse
(causalscenario(2)inFig.2).Evidencegatheredsofarsuggeststhefollowingmodel:IntheabsenceofABA,PP2C-Aphosphatasesmaintainanactive,de-phosphorylatedstateofBRM
therebypreventingexpressionofABA-responsegenes.UponanABAsignal,ABA-receptorsbindPP2Cs.PP2CsareremovedfromBRM,andBRMisphosphorylatedbySnRKkinases,
whichleadstoitsinactivation.InactivationofBRMreleasestherepressionoftheABA-induciblegenes.TheexactmodebywhichBRMrepressesthetargetlociremainstobe
determined,butmayinvolvenucleosomerepositioning.Fordetailsandreferencesseemaintext.
112 M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122
2.3.1.Histonede-/acetylationatstress-responsivegenesofArabidopsis them beingRXT3. AnArabidopsishomolog of RXT3named Histone
Inresponsetoadehydrationtreatmentlastingfrom1to5h,known DeacetylaseComplex1(HDC1)wasfoundtobeabletodirectlyinteract
drought-responsivegenessuchasRD29A,RD29B,RD20andRAP2.4were withthehistonedeacetylasesHDA6andHDA19andtoaffectstress
foundtobedifferentiallyacetylatedatK9,K14,K23andK27ofhistone3 sensitivity of seedlings [108]. Similar to hda6 and hda19 mutants
inA.thaliana[99].Higherlevelsofhistoneacetylationcorrelatedwith [109],thehdc1knockoutmutantseedlingsdisplayedhypersensitivity
anincreaseingenetranscriptionwithin2–5hafterthetreatment.The toABAandNaCl[108].OverexpressionofHDC1resultedinABA/salt
levelsofH3K9AcinRD20andRD29Awerealsomonitoredoveratime hyposensitivity. No phenotypes have been reported for plants
course of several hours after recovery from drought stress [100]. overexpressingtheHDAsinA.thaliana,indicatingthatHDC1isarate-
H3K9Ac,whichwasincreasedduringdrought,wasquicklyreduced limitingcomponentofHDACcomplexes.Inaccordancewiththisnotion,
afterrehydration.Inadditiontothetypicaldroughtstressmarkers lossofhdc1ledtoanincreaseofH3K9/K14acatthetotalproteinlevel,
RD29A/B,whichhaveunknownfunction,acetylationlevelsofH3K9/ whichwasreversedaftercomplementationwithgenomicHDC1.At
K14werealsomonitoredforgenesencodingproteinsofknownfunc- single-genelevel,genesencodingABAbiosyntheticenzymes(ABA1),
tion,includingthetranscriptionfactorDREB2A,theproteinphospha- drought-repressed proteins (DR4) and ABA receptors (PYL4) were
tasesABI1andABI2,andthepotassiumchannelsKAT1andKAT2[101, hyper-acetylatedinhdc1-1andhypo-acetylatedinHDC1overexpress-
102].ABI1andABI2wereinducedbyABAandNaCl,whereastranscript inglines,respectively,andtheirtranscriptlevelsfollowedtheexpected
levelsofKAT1andKAT2onlyincreasedinresponsetoABA.InChIPex- patternwithoverallhigherorlowertranscriptlevels,respectively.The
perimentsasalt-inducedincreaseofH3K9/K14acetylationwasfound resultsidentifyHDC1asanimportantfactorcontrollingtheapparent
forABI2andRD29Batthefirstexon,whileadecreasewasrecordedat activity of HDAs and fine-tuning histone acetylation during stress
thepromoterregionofABI2,andnochangewasfoundforABI1,KAT1 responses.Inafollow-upstudyitwasfoundthatHDC1notonlydirectly
andKAT2.ThesestudiesshowedthatstressaltersH3K9/K14Aclevels bindstoHDAsandH3-bindingproteinsbutalsotoH1variants,suggest-
ofsomegenes,buttheydidnotrevealifandhowlocaldifferences inganovelroleforlinkerhistonesintranscriptionalgenerepression
mayimpactontranscriptionalstressresponses. underabioticstress[66].
In an independent study, HDC1 was confirmed as member of a
2.3.2.Stress-relatedphenotypesofhistonedeacetylasemutants nativeproteincomplexinA.thalianacontainingHDA19[110]andthe
Amoremechanisticinsightintotheroleofhistonede-/acetylation H3-bindingproteinMSI1[111].ABAresponsivegenessuchasRD29B,
canbeexpectedfrommutantanalysis.Analysisofhda6mutants,defec- ANACO19andCOR15A,aswellasABAreceptorsPYL4,PYL5andPYL6,
tiveforhistonedeacetylaseHDA6[102],revealedhigherH3K9/K14ac showedhighertranscriptlevelsinmsi1,hda19andmsi1/hda19knock-
levelsthaninwildtypeincontrolconditionforsomeloci,butthere outplantsthaninwildtype.Atthechromatinlevel,PYLgenesdisplayed
wasnoclearcorrelationwiththetranscriptlevels.Moreimportantly, increasedH3K9acetylationaroundthetranscriptionalstartsite,and
salt-inducedhyper-acetylationofDREB2AandRD29Awaslostinhda6 ChIPexperimentsindicatedthatMSI1wasabletophysicallyassociate
mutantsandtranscriptionalup-regulationwasattenuated,suggesting withthePYLgenesequencesaroundthesamepositions.Itislikely
that HDA6 is required for both responses. Knockout of the HDA6- thattheinteractionismediatedbyotherproteinsinthecomplex,inpar-
interactingputativedeacetylaseHD2CinArabidopsisalsoledtoanin- ticularco-repressors,buttheseremaintobeidentified.Basedontheir
creaseofH3K9/K14acetylationlevels,forexampleinABI1andABI2 homology to yeast co-repressors, SIN3-like proteins that co-eluted
[103].InaccordancewitharequirementofABI1/2forABA-sensing withHDA19andMSI1[110]aregoodcandidates.Infact,AtSIN3had
[104],hd2cmutantsdisplayedahypersensitiveresponsetoABAor previouslybeenshowntointeractwithHDA19andwiththeethylene
NaCl during germination [103]. Conversely, plants overexpressing responsiverepressivetranscriptionfactorERF7[112].
HD2CwerefoundtobelesssensitivetoABAorNaClduringgermination HATscatalysehistoneacetylationtherebypotentiallyfacilitating
[105].Thefindingsindicateapotentialmechanisticlinkbetweenhis- genetranscription.TheA.thalianaHATGCN5formsacomplexwith
tonedeacetylationandABAsignalling,wherebyhistoneacetylation thetranscriptionalco-activatorsADAandSAGA[113].Lossoffunction
levelsofimportantABA-signalingcomponentsdeterminethesetpoint mutants ada2b and sfg29 show reduced salt sensitivity and lower
of ABA sensitivity. One would expect then that knockout of the expressionofknownsalt-responsivegenes,includingRAB18,COR6.6,
deacetylasesnolongerincreasesABAsensitivityinanabi1/2back- RD29B[114].ChIP-PCRsamplingofH3K9/K14andH4K5/K8/K12/K16
ground,andthisneedstobetestedinthefuture.Furthermore,thetran- acetylation levels at promoter regions indicated that knockout of
scriptionalresponsesofABA-responsivedownstreamgenesshouldbe ADA2baffectsallofthesemarksatRAB18andCOR6.6,butonlyH3K9/
assessedinhda/abidoublemutantstointerrogatecausalrelationships K14Ac at RD29B [114]. This suggests that the residues targeted by
betweenhistoneacetylationandtranscriptionalresponses. HATsdependonlocalsequenceandchromatinenvironment.
Recently,histonedeacetylase9(HDA9)wasreportedtorepress Overall,thereisstrongevidencethatHDAsandHATsareanintegral
stress-responsivegenes[106].Transcriptomeanalysisofhda9mutants partoftranscriptionalregulation,asdepictedinFig.5A.Theyarerecruit-
revealedincreasedexpressionofgenesinvolvedinplantresponsesto edtotheDNAthroughco-activators/repressorsandfurthermodulated
waterdeprivation.FurthermoreChIPanalysisofplantssubjectedto intheirapparentactivitybyadditionalfactorswithinmulti-protein
saltordroughtstressesshowedH3K9hyperacetylationat14selected complexes.Theirrelativeactivitiesdetermineacetylationlevelsand
genesinhda9mutantscomparedtowildtype[106].Surprisingly,at responsivenessofthegenes(andtheplant)toabioticstressessuchas
phenotypiclevel,hda9seedlingsshowedlesssensitivitytosaltand saltanddrought.However,muchmoreresearchisrequiredtounder-
PEG during germination than wildtype. They had longer roots and standwhetherplants(1)activelymakeuseofthissystemtoadjust
highergerminationrates,andhencetheoppositephenotypeofother thesetpointofstresssensitivity,e.g.afterpriming,orinresponseto
histonedeacetylationmutants(seeabove).Thefindingsexemplifythe multiplestresses,and(2)dynamicallyre-assembleHAT/HDAcom-
factthattranscriptionalrepressionbyhistonedeacetylasescanhavedif- plexestoswitchbetweendifferentsetsoftargetgenes.
ferentphenotypicconsequencesdependingonthespecificsetoftarget
genes. 2.3.4.Stress-responsivehistoneacetylationmarksincrops
In addition to experiments carried out with the model plant
2.3.3.Proteinpartnersofhistonede-/acetylases A. thaliana several studies of histone acetylation/deacetylation in
Histonedeacetylasesformcomplexeswithmultipleotherproteins responsetostresswereperformedoncrops.Inmaize,salttreatment
whichhavebeenbiochemicallycharacterisedinyeast[107].Alongside ofrootsinhydroponicscausedaglobalincreaseofH3K9andH4K5acet-
co-repressors and histone-binding proteins, several proteins of ylationandtranscriptionalup-regulationofexpansinsandothercell
unknownfunctionco-elutedwiththeyeastRPD3deacetylase,oneof wall-relatedgenes.Amongthese,ZmEXPB2andZmXET1hadincreased
Table1
Listofselectedstudiesthathaveanalysedhistonemodificationsandgeneexpressionunderabioticstress.Thetableincludesthespeciesandgenotype,thespecifichistonemodificationsmonitored,thestresstreatmentapplied,thedurationofthe
treatmentandtimepointsanalysed,andthetechniquesusedtomeasurethechromatinmarks(ChIP-sequencing,ChIP-qPCR,Westernblot)andgeneexpression(RNA-sequencingormicroarray,RT-qPCR).
Species,genotype Chromatinmarkstested Stress Time Genestested ChIP-seq ChIP-qPCR RNA-seq/microarray RT-qPCR Western Ref
M
blot .-A
.
A.thalianaCol-0 H3K9ac,H3K14ac,H3K23ac, Drought 1,2,5h RD29A,RD29B,RD20,RAP2.4 X X [99] Ase
H3K27ac,H3K4me3 n
A.thalianaCol-0 H3K9ac,H3K4me3 Drought 4h;rehydrationfor1–5h RD20,RD29A,AtGOLS2,ProDH X X [100] si-Fa
(timecourse) ba
A.thalianaaxe1-5Col-0, H3K9K14ac,H3K4me3, ABA,NaCl 5days ABI1,ABI2,RD29A,RD29B,KAT1,KAT2, X X [102] do
CS24039(HDA6RNAi)Ws H3K9me2 DREB2A et
a
A.thalianaaxe1-5,hd2c-1, H3K9K14ac,H3K9me2 ABA,NaCl 5days ABI1,ABI2,ERF4 X X X [103] l.
/
hd2c-3Col-0 Bio
A.thaliana35S::HD2C-GFP ABA,NaCl, 5–20days RD29B,RAB18,ABI2,ADH1,KAT1,KAT2,SKOR X [105] ch
Col-0 Mannitol im
A.thalianahda9-1,hda9-2 H3K9ac NaCl,KCl, 6–78h Genome-wide X X [106] ica
e
Col-0 Mannitol tB
A.thalianahdc1-1,35::HDC1, H3K9K14ac NaCl 24h ABA1,RD29B,PYL4,DR4,ABA3,RD29A,AFP3, X X X [108] iop
h
Ubi10::HDC1Col-0 RAB18 y
A.thalianahda19-1Ws ABA,NaCl 5days ABI1,ABI2,RD29B,KAT1,KAT2 X [109] sica
A.Cthoal-l0ianahda19,msi1–as H3K9ac ABA,NaCl (4N–1aC0lh)(ABA);0–70h RD29B,ANACO19,COR15A,PYL4,PYL5,PYL6 X X [111] Acta
1
A.thalianaada2b-1,gcn5-1 Cold 21hto2days Genome-wide X [113] 86
0
A.Wthsalianaada2b-1,gcn5-1, H3K9K14ac,H4ac NaCl (3t–im12ehc,o5urdsaey)s RAB18,COR47,COR78,COR6.6,RD29B,COR15 X X [114] (201
ada2a-2,sgf29a-1Ws (K5,K8,K12,K16) (germination) 7)
1
Zeamays H3K9ac,H4K4ac NaCl 7days ZmExPA1,ZmEXPA3,ZmEXPA5,ZmEXPB1, X X X [115] 0
6
ZmEXPB2,ZmEXPB4,ZmXET1 1–
Hordeumvulgare ABA,SA,JA 6–24h HvHDAC2-1,HvHDAC2-2 X [116] 22
Oryzasativa H3K18ac,H3K27ac,H4K5ac, Drought 0–33h(timecourse) OsHAC703,OsHAG703,OsHAM701,OsHAF701 X X [117]
H3K9ac
Oryzasativa ABA,NaCl 5–14days OsGA20ox2,OsGA20ox3,OsGA3ox1 X [118]
(continuedonnextpage)
1
1
3
1
1
4
Table1(continued)
Species,genotype Chromatinmarkstested Stress Time Genestested ChIP-seq ChIP-qPCR RNA-seq/microarray RT-qPCR Western Ref
blot
ZmUbi10::HDA705
A.thalianaaxe1-5Col-0, Cold 3daysacclimation, Genome-wide X [120]
sil1Ler 3hfreezing
Zeamays H3K9ac,H4K5ac,H4K4ac Cold 15minfreezing ZmDREB1,ZmICE1,ZmCOR413 X X X [121]
M
Zeamays H3K9ac Cold (3t–im6weceoeuksrse) Genome-wide X [122] .-A.
A
Oryzasativa H3K9ac,H3K9K14ac,H3K27ac Cold 2–16h(timecourse) OsDREB1 X [123] se
n
A.thalianaCol-0 H3K4me3,H3K4me2,H3K4me1 Drought (4t–o6RdWayCs*65%) Genome-wide X X [129] si-Fa
b
Oryzasativassp.japonicacv. H3K4me3 Drought ToRWC50% Genome-wide X X [130] ad
o
ZH11 e
t
A.thalianaatx1,35S::ATX1 H3K4me3 Drought 12days NCED3,RD29A,RD29B X X [131] al.
atx1Ws /B
A.thalianaatx1Ws, H3K4me3 Dehydration 2h+22hrecovery,4 RD29A,COR15A,RD29B,RAB18 X X [132] ioch
areb1areb2abf3 cycles im
A.thalianajmj15-1,jmj15-2, H3K4me3,H3K4me2,H3K4me1 Salt 1h RD29A,RD29B,RD22,COR15A,COR47, X X [133] ica
jmj15-3,JMJ15::GUS, P5CS1,P5CS2 et
B
35S::JMJ15-HACol-0 io
p
A.thalianaCol-0 H3K27me3 Salt 24h Genome-wide X X X X [65] h
y
A.thalianaflc-3,jmj32-1, H3K27me3 Heat 8days FLC X X X X [125] sica
jmj30-1,jmj30-2, A
jmj30-2jmj32-1, cta
35S::JMJ30-HA, 18
6
35S::JMJ32-HACol-0 0
A.thalianaCol-0 H3K27me3 Cold 6days;2/1/1/days COR15A,ATGOLS3 X X [136] (20
stress/recovery/stress 17
)
Oryzasativacv.Nipponbare H3K4me3,H3K4me2, Submergence 24h OsADH1,OsPDC1 X X [137] 1
0
H3K9/14ac 6–
A.thalianahsfa2-1, H3K4me3,H3K4me2,H3K9ac Heat 1–3hacclimation, APX2,HSP18.2,HSP22.0,HSP70 X X [140] 12
2
pHSFA2::HSFA2-YFPCol-0 repeated.
A.thalianasid2-1,npr1-1, H3K4me3/2,H3K9/14ac Heat,cold,salt, 1.5hperday(forupto7 WRKY53,FRK1,NHL10 X X [141]
ein2-1, P.syringae days)
coi1-16,hac1-1
Col-0/Col-6
*RWC:relativewatercontent.
M.-A.Asensi-Fabadoetal./BiochimicaetBiophysicaActa1860(2017)106–122 115
H3K9ac at the promoter regions [115]. Two histone deacetylases expression[119],andhistonede-/acetylationhasbeenproposedto
HvHDAC2-1andHvHDAC2-2,wereisolatedfrombarleyandfoundto playamajorroleinthisprocess[120].Inmaize,shorttreatmentswith
transcriptionallyrespondtoABA,SAandJA[116].Inriceplantsexposed coldtemperaturesdecreasedhistoneacetylationatpositionsH3K9,
to drought stress,theexpression of fourhistoneacetyltransferases H4K5andH4K4atthetotalproteinlevel[121].Theeffectwasreverted
(OsHAC703,OsHAG703,OsHAF701andOsHAM701)wasfoundtobe whentheplantswerereturnedtocontroltemperature.ZmDREB1isthe
significantlyincreased.Thetranscriptionalresponsewasmatchedby majortranscriptionfactorinducedbycold,togetherwithitstargetgene
higherH3K9/K18/K27andH4K5acetylationatthetotalproteinlevel ZmCOR13. After treatment with the histone deacetylase inhibitor
[117].OverexpressionofthericehistonedeacetylaseHDA705decreased trichostatinA(TSA),ZmDREB1wasnolongerinducedbycold,suggest-
seedgerminationinresponsetoABAorsalt,thusreflectingphenotypes ingthatZmDREB1inductionrequireshistonedeacetylation,although
ofArabidopsismutantsrelatedtoHDA6andHDA19.Inthiscase,the notnecessarilyinthesamegene.Anothercold-inducedtranscription
lowergerminationratewasattributedtodecreasedtranscriptlevelsof factor,ZmICE1wasnotaffectedbyTSA.AnalysisoftheH3K9,H4K5
theGAbiosyntheticgenesOsGA20ox2,OsGA20ox3,OsGA3ox1[118].In andH4-tetraacetylationintheDREB1promoterregionsindicatedthat
general,causalrelationshipbetweenhistonedeacetylation,transcript aftercoldacclimationDREB1DNAsequencesthatareusuallybound
levelandphysiologicalresponsesremaintobeproven,however,the byICE1werehyper-acetylatedwhileadjacentregionswhicharenot
observedtranscriptionalregulationoftheHDAsareinteresting.Inour involvedinICE1bindingwerenot.UponcoldtreatmentwithTSA,all
tentative model (Fig. 5A), induction of HDAs in response to stress regions were hyper-acetylated compared to control conditions.
wouldde-sensitizetheplant,leadingeithertotransientresponsesto Theseresultsindicateapositiveregulatoryroleofhistonedeacetylation
theinitialstressortoalowerresponseuponstressre-occurrence. on DREB1 induction during cold-acclimation, which is somewhat
Inadditiontodroughtandsalt,lowtemperatureisoneofthemajor counter-intuitive given the assumed repressive action of histone
environmentalstressesthatcauseagriculturalyieldloss.Plantsareable deacetylation.Itispossiblethattheobservedlocaldifferenceshyper/
toincreasetheirfreezingtoleranceafterexposuretoshortand/ormod- hypo-acetylation explain this effect. A subsequent study assessed
erate chilling. Cold acclimation involves re-programming of gene thegenome-wideeffectofcoldonH3K9acetylationinmaize[122].
A Transcriptional
H binding, reading
regulation
Co-factors
HDA
Co-repressor
Stress-regulated genes
Drought, TF repressive -
H3K9/14ac Transcription Response
salt, cold TF activating +
(e.g.RD29B, RAB18 )
Co-activator
HAT
Co-factors
H binding, reading
B ‘Non-trainable’ genes ATX1,
(e.g. RD29A) Pol-II
recruitment
1.
Transcriptional
Desiccation
regulation
H3K4me3,
Water
repeated Pol-II Transcription
retention
progression
‘Trainable’ genes
(e.g. RD29B)
Fig.5.Roleofhistonemodificationsinstressresponses.A:Histonede-/acetylation:Histoneacetyl-transferases(HATs)anddeacetylases(HDAs)areanintegralpartoftranscriptional
regulation.ThecurrentstateofknowledgesuggestsamodelinwhichtheenzymesarerecruitedtotheDNAbystress-regulatedtranscriptionfactors(TFs)throughco-activatorsand
co-repressors,andfurthermodulatedintheirapparentactivitybyadditionalfactorswithinmulti-proteincomplexes(forfurtherdetailsonindividualproteinsseemaintext).The
relativeactivityofHATsandHDAsdetermineshistoneacetylationlevelsatthetargetlociandtranscriptionalactivity,withdownstreameffectsonplantresponses.However,specific
pairsofTFsandco-activators/repressors,aswellastheexactcompositionofnativemulti-proteincomplexes,needtobeidentifiedtounravelprecisecausalrelationshipsbetween
histonede-/acetylation,transcriptlevelsandphysiologicalresponses.TranscriptionalinductionofHDAsinresponsetostress,asobservedinsomecropspeciescouldprovideameans
toterminatetranscriptionalresponsesortodesensitizetheplanttorepeatedstress.Histone-bindingproteinsinHATandHDAcomplexeshave‘reading’functiontherebyguidingthe
enzymestocertainhistonemarkssuchasH3K4me3.B:Histonede-/methylation:Experimentsinvolvingrepeatedexposureofseedlingstodesiccationfollowedbyrecoveryperiods
haveledtoamodelforshort-termstressmemorybasedonestablishmentandmaintenanceofH3K4me3marks.Inthismodel,chromatinprocessessuchasproteinrecruitmentand
histonemethylationareassociatedwithdifferentphasesoftranscription,namelyinitiationandelongation.Insomegenes,socalled‘trainable’or‘memory’genes,H3K4me3deposited
duringthefirststressresponseisretainedforsometimeafterstressrelief,andPol-IIisstalledattheinitiationcomplex.Thisformationthenfacilitatestranscriptelongationwhenthe
stressre-occurs,leadingtohyper-inductionofthegenes.Thephysiologicaleffectisimprovedwaterretentionduringthesubsequentstressevents.Thefactorsthatdeterminewhether
aparticularstress-inducedgenehasatranscriptionalmemoryornotremaintobefurthercharacterised.Fordetailsandreferencesseemaintext.