Nutrient stress-induced chromatin changes in plants

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Nutrient stress-induced chromatin changes in plants

David Secco, James Whelan, Hatem Rouached, Ryan Lister

To cite this version:

David Secco, James Whelan, Hatem Rouached, Ryan Lister. Nutrient stress-induced chro- matin changes in plants. Current Opinion in Plant Biology, Elsevier, 2017, 39, pp.1-7.

�10.1016/j.pbi.2017.04.001�. �hal-01594549�

Nutrient stress-induced chromatin changes in plants David Secco

, James Whelan

, Hatem Rouached

and Ryan Lister

Theabilityofplantstoappropriatelyrespondtothesoilnutrient availabilityisofprimaryimportancefortheirdevelopmentand tocompletetheirlifecycle.Decipheringthesemultifaceted adaptivemechanismsremainsamajorchallengeforscientists todate.Recenttechnologicalbreakthroughsnowenableto assessthedynamismandcomplexityoftheseprocessesat unprecedentedresolution.Inthisreview,wepresentsomeof themostrecentfindingsontheinvolvementofhistone modifications,histonevariantsandDNAmethylationin responsetonutrientstressesaswellasdiscussingthepotential rolesthesechromatinchangescouldserveasprimingoras trans-generationalstressmemorymechanisms.

Addresses

1ARCCentreofExcellenceinPlantEnergyBiology,TheUniversityof WesternAustralia,Perth,Australia

2BiochimieetPhysiologieMole´culairedesPlantes,CNRS,INRA, MontpellierSupAgro,UM,Montpellier,France

3DepartmentofAnimal,PlantandSoilScience,SchoolofLifeScience, ARCCentreofExcellenceinPlantEnergyBiology,LaTrobeUniversity, Bundoora,Australia

Correspondingauthor:Secco,David([email protected])

CurrentOpinioninPlantBiology2017,39:1–7

ThisreviewcomesfromathemedissueonCellsignallingandgene regulation

EditedbyTzyy-JenChiouandToruFujiwara

http://dx.doi.org/10.1016/j.pbi.2017.04.001

1369-5266/ã2017TheAuthors.PublishedbyElsevierLtd.Thisisan openaccessarticleundertheCCBY-NC-NDlicense(http://creative- commons.org/licenses/by-nc-nd/4.0/).

Introduction

Because of their sessile nature, plants can adjust their growth and development in response to amultitude of environmental cues such as light quality, temperature, photoperiod and nutrient availability. This plasticity allowsthemtoadapttotheirlocalandchangingenviron- ment, providingtheoptimumresponses to acclimateto these challenges. Nutrient availability, like other envi- ronmentalcues,isperceivedandtransmittedbyamulti- tudeofsignallingpathways,ultimatelyenablingplantsto bettercopewithdynamicandchallengingenvironments.

In recent years, numerous studiesranging from pheno- typic to molecular analyses have greatly improved our understanding of the complex regulatory networks

involved in these mechanisms [1–8]. Among these, sophisticated dynamic changes in chromatin structure have been observed in response to numerous environ- mental conditions, often associated with concomitant changes in geneexpression (reviewed in Refs. [9–14]).

Thebasicchromatinunitisconstitutedof147basepairs of DNA wrapped around the eight core histones and formsthe nucleosome. Chromatinremodellinginvolves therearrangementofchromatinbetweencondensedand transcriptionally quiescent andaccessible and transcrip- tionallypermissivestates,modulatingtheabilityoftran- scriptionfactorsorotherDNAbindingproteinstoaccess DNAandcontrolgeneexpression.Biochemicalchanges in chromatin state include histone modifications and histone variants as well as DNA methylation, which can be dynamically changed to maintain gene and genome activities. The capacityof some of thesemod- ificationstobestablytransmittedthroughmitosisaswell asmeiosisledtothehypothesisthatchangesinchromatin statecouldserveasstressprimingand/ormemorymech- anisms to preparefuture generationsto efficiently cope withbioticandabioticstresses(forreviewseeRefs.[14–

17]).However,todateveryfewexperimentallyvalidated casesofmitoticormeiotictransmissionofstressinduced changes in chromatin structure have been reported in plants. Thus it is important to clearly distinguishchro- matin changes from epigenetic changes. Indeed both terms are frequently used to designate any changes in chromatin structure, independently of any notion of heritability[9].Inthisreview,thetermepigeneticsrefers to heritable patterns of phenotypic variation, that is, stable transmission of information through mitosis or meiosis thatarenotsolelyattributable todifferencesin DNAsequence.Indeed,stress-inducedchangesinchro- matin structure may play critical roles in the plant response to this condition without necessarily leading to mitotic or meiotic heritable changes. The field of chromatin research has greatly benefited from high- throughput next generation sequencing technologies, the availability of qualityantibodies for modified DNA or histone residues, as well as improved genome sequencesandannotations,enablingassessmentofchro- matinchangesatthewholegenomelevelandatunprec- edented resolution. As a result, changes in chromatin structurehavebeenobservedinresponsetoamultitude ofconditions,includingabioticstresses,suchasdrought, salt stress, and temperature (for review see Refs.

[12,13,18–20]). To date, vernalization likely represents the best-understood example of environmentally induced chromatin changes (for a detailed review, see

Ref. [21]). These modifications in chromatin state are heritable and are hence considered epigenetic. While chromatinmodificationsare integralto some epigenetic phenomena,somecasesof chromatinchangesarelikely notheritableand are thus notconsideredas epigenetic [22].Todate,onlyasmallnumberofstudieshavefocused ontheroleofchromatinregulationinresponsetochanges in nutrient availability, and thus its potential role in regulatingnutrienthomeostasis(Tables1and2).Inthis article,wewillprovideareviewofthecurrentstateofthe fieldaswellasdiscussingpotentiallimitationsandfuture directions.

Histone modifications

Histonesaretheproteincomponentsofthenucleosomes thatformthebasicarchitectureofeukaryoticchromatin.

Eachnucleosomeiscomprisedofanoctamericcomplex containingtwocopieseachofthehistonesH3,H2A,H2B andH4,andistypicallyenfoldedby147bpofDNA[23].

EachhistonehasbothaC-terminalhistone-foldandaN- terminal tail, with theN-terminal tails being preferen- tiallysubject to avariety of post-translational modifica- tions,suchas acetylation,phosphorylation,methylation, ubiquitination, and ADP-ribosylation, as well as other poorlystudiedoryetunknownmodifications[24].These modificationsarereversibleandmaintainedbytheaction of a variety of histone modifying enzymes, influencing chromatin structure and hence playing an important regulatory rolein processessuch as transcription,DNA repair,andreplication.Todate,mostoftheinvestigation ofhistonemodificationsdynamicsinresponsetonutrient stresseshavefocuseduponhistonemethylation.In2011, Widiezetal.characterizedthehighnitrogen-insensitive9-1 (hni9)mutantthatisimpaired inthesystemicfeedback repressionoftherootnitratetransporterNRT2.1byhigh

Nsupply,revealingthatHNI9/AtIWS1wasakeyfactor inthedepositionoftrimethylatedlysine27ofhistoneH3 (H3K27me3)attheNRT2.1locusinresponseto highN supply[25].Morerecently,ithasbeenshownthatsym- metricdimethylationofhistone H4R3(H4R3sme2)was involvedin ironhomeostasis [26].Indeed, mutation in the Arabidopsis Protein Arginine MethylTransferase 5 (PRMT5,alsoreferredtoasSKB1),involvedincatalyzing histone H4R3 symmetric dimethylation, resulted in mutantplantshavinghigherironaccumulationinshoots and greater tolerance to iron deficiency than wild type plants.MutationinPRMT5alsoaffectedtheexpressionof several Ib subgroup bHLH genes [26], which are requiredfortheregulationofironuptakeandhomeostasis inArabidopsis[27]and iron-uptakeprocesses[26].The involvement of trimethylated lysine 4 of histone H3 (H3K4me3) in response to nutrient stress was also reportedinastudyaimedatidentifyinggenesinvolved in root hair elongation in Arabidopsis specifically under phosphatestarvation,revealingthealfin-like6(AL6)gene [28,29]. AL6 contains a Plant Homeo Domain (PHD) finger that canbind to H3K4me3 [30], thus qualifying AL6as a bonafide histonereader.AL6 isnon-transcrip- tionally responsive to Pi starvation and the al6 mutant plants displayed a pleiotropic phenotype including reducedanthocyaninaccumulationandalteredrootarchi- tectureinresponsetolowPi,namelyveryshortroothairs.

SinceH3K4me3isthoughttobeabindingplatform for transcriptional activators and for factors that mediate transcriptelongationandmRNAmaturation,theauthors suggestedthatAL6couldaffecttranscriptmaturationand stabilityofcriticalgenesinvolvedinroothairelongation [28,29].Arecentstudyfromthesamegrouprevealedthat histone acetylation was involved in Pi homeostasis, through the investigation of the Arabidopsis histone

2 Cellsignallingandgeneregulation

Table1

Summaryofchromatinchangesaffectinghistonesinresponsetonutrientavailability

Chromatinchange Stress Gene Function References

Histonemodifications

H3K27me3 N AtHNI9 InvolvedinthedepositionofH3K27me3attheNRT2.1locusin responsetohighNsupply

[25]

H4R3sme2 Fe AtPRMT5 Negativelyregulatesironhomeostasis,viaregulationofIb subgroupbHLHgenes

[26] H3K4me3 P AtAL6 Affectstranscriptmaturationandstabilityofcriticalgenesinvolved

inroothairelongation

[28,29]

Acetylation P AtHD19 InvolvedincontrollinginbothPideficientandsufficientconditions aswellasbeinginvolvedinregulatingasubsetofkeyphosphate starvation

[31]

H3K9ac,H3K14ac Fe AtGCN5 MajorroleinFRD3-mediatedironhomeostasis [32]

Histonevariants

H2A.Z P ARP6 RequiredforproperdepositionofH2A.ZatnumerouskeyPi

starvation-inducedgenesinresponsetoPistarvation

[34]

H2A.Z P IPK1 InvolvedinthetranscriptionalregulationofsomePistarvation- responsivegenes

[38]

deacetylase 19(HD19)[31].Indeed, characterizationof theArabidopsisHD19mutantandover-expressingplants revealed a key role of HD19 in controlling root cell elongationin bothPideficientandsufficientconditions as wellas beinginvolved in regulating a subset of key phosphate starvation induced genes, including some of theSPXgenesinvolvedinPisensingandsignalling[31].

Anadditionalcaseofhistoneacetylation-regulatednutri- enthomeostasiswasrecentlydiscoveredwiththeobser- vation that mutation of the histone acetyltransferase GeneralControl Non-repressed5 (GCN5)generesulted inimpairedirontranslocationfromtheroottotheshootin Arabidopsis[32].Inthisstudy,theauthorsrevealedthat GCN5 coulddirectlybindtothepromotersoffiveiron- related genes, including Ferric Reductase Defective 3 (FRD3),akeyfactorinvolvedinironnutritionmodulate theiracetylationlevelsofhistone3lysine9(H3K9ac)and histone3lysine (H3K14ac)levels,andin turnregulates theirtranscriptexpression[32].

Histone variants

Histone variantsare non-canonical(non-allelic) variants ofhistonesthatpossessoneorseveralamino-aciddiffer- ences,andthathavespecificexpression,localizationand species-distribution patterns. The incorporation of his- tone variantsin thenucleosomecanconfernovelstruc- tural and functionalpropertiesonthenucleosome, ulti- mately affecting chromatin remodelling and gene expression[33].Amongthecorehistones,theH2Afamily is themostdiverse, and theSWR1chromatin-remodel- ling complexis involvedin replacing thecanonical his- tone H2Awith theH2A.Zvariant atspecific chromatin regions.In2010,Smithetal.[34],demonstratedthatthe Arabidopsisnuclearactin-relatedprotein6(ARP6),akey component of SWR1 [35,36], was required for proper H2A.ZdepositionatnumerouskeyPistarvation-induced genes in response to Pi starvation. Indeed, mutation of

ARP6resulted in theloss of H2A.Zatmanyphosphate starvation induced genes and resulted in depression of these genes under Pi replete conditions [34]. Similar observations were also seen in yeast, where the SWR1 complex hasbeen implicated in controlling theexpres- sionlevelsofnumerousPiresponsivegenes,suchasthe PHOgenes[37].TheinvolvementofH2A.Zinregulat- ingPihomeostasis inplantshasrecentlybeenstrength- ened through the study of the role of the Arabidopsis inositol pentakisphosphate 2-kinase coding gene (AtIPK1) that is involved in the biosynthesis of phytic acid, the main source of P in the seed [38]. Indeed, mutation ofIPK1 resulted in numerousphosphate star- vation-inducedgenesbeinginduced,andcorrelatedwith a reductionof histone variant H2A.Zoccupation in the chromatinattheseloci[38].

DNAmethylation

DNAmethylationisacovalentandstablemodificationof cytosineingenomicDNAthatcaninfluencegeneexpres- sionandtransposonactivity[39].Inplants,itreferstothe formationof5-methylcytosinefromcytosinethroughthe action ofaDNAmethyltransferase,andcanoccurin all three DNA sequence contexts: CG, CHG and CHH, where His anynucleotide except guanine.Since DNA methylationisoftenmitoticallyandmeioticallyheritable [39], it has been hypothesized that it could serve as a stress memory mechanism, with stress-induced DNA methylation changes being maintained through mitotic and/or meiotic cellular division and thus acting as a priming mechanism to prepare future generations to efficiently cope with biotic and abiotic stresses. In 2011, Kou et al. used methyl-sensitive AFLP (MSAP) to identify changes in DNA methylation in rice plants growingunderdifferentnitrogenlimitingconditions[40].

Despite identifying changes in DNA methylation that couldbetransmittedtothenextgenerationofplants,the

Table2

SummaryofnutrientstressrelatedchangesinDNAmethylation

Stress Method Organism Role References

N MSAP Rice ChangesinDNAmethylationthatcouldbetransmittedtooffspringandprovide enhancedtolerancetostress

[40]

P WGBS Rice MainlytransientchangesinDNAmethylationofTEsinthevicinityofPi-stressed inducedgenes

Notransgenerationaltransmission

CausalitybetweenchangesinDNAmethylationandgeneexpression

[42]

P WGBS Arabidopsis LimitedchangesinDNAmethylationobserved,associatedwithPistarvation- induciblegenes

[42] P WGBS Arabidopsis ExtensivechangesinDNAmethylationassociatedwithchangesingene

expression

DifferentialmethylationnearbyPiresponsivemotifproposedtoregulateTF bindingandgeneexpression

[43,44]

S WGBS Arabidopsis MutationofMSA1affectsgenome-wideDNAmethylationincludingthe methylationofSdeficiencyresponsivegenes

DifferentialmethylationnearbySresponsivemotifproposedtoregulateTFbinding andSdeficiencyresponsivegeneexpression

[47]

approachusedhaslimitationsinquantifyingDNAmeth- ylation changes and is often inconsistent [41]. Using whole genomebisulphite sequencing to generate base- resolution maps of DNA methylation throughout the genome, two recent studies revealed that phosphate starvationcouldinducenumerouschangesinDNAmeth- ylation[42,43].Inthefirststudy,Seccoetal.showed thatphosphate starvationin rice resultedin widespread transientchangesin DNA methylation, mainlythrough hypermethylationoftransposableelements(TEs)inthe vicinityof Pi-stressed induced genes. While it is often assumedthatchangesinDNAmethylationdrivechanges in genes expression, this study clearly established the causality in this relationship, whereby changes in tran- scriptabundanceprecededlocalchangesinDNAmeth- ylation[42].Inaddition,thisstudyassessedthepoten- tialstress-memorymechanism,revealinglimitedstability ofsuchinducedDNAmethylationeventsthroughmito- sis,andtheabsenceoftheirtransmissionthroughmeiosis [42].Surprisingly,using asimilarexperimental design inArabidopsisrevealedalimitednumberofPistarvation inducedchangesinDNAmethylation,proposedtobea consequenceofalowertransposableelement (TE)con- tent compared to rice [42]. Yong-Villalobos et al.

recentlyreportedthatPistarvationinArabidopsisresulted inextensiveremodellingofglobalDNAmethylationthat oftencorrelatedwithchangesinatranscriptabundanceof key phosphate starvation induced genes and that the expression of genes encoding DNA methyltransferases appeared to bedirectly controlled bythe key regulator PHOSPHATERESPONSE 1 (PHR1) [43]. The dis- crepancies observed between the two studies could potentiallybeattributedtodifferencesintheexperimen- taldesignsuchasthelengthandextentofthePistarva- tion treatment, but are most likely theresult of differ- ences in identifying and calling the changes in DNA methylation. Indeed, to date, there is no consensuson what constitutes a differentially methylated region (DMR),that iswhatistheminimum numberof differ- entially methylated cytosines (DMC) a DMR should contain, the maximum distance between neighbouring DMCs,thefoldchangeforeachDMCandfortheDMR?

Inaddition,verylittleinformationexistsontheeffectof DMRs on nearby gene expression, that is, is there a minimum number of DMCs required to regulate gene expression or aminimum foldchange in DNAmethyl- ation,aswellasthedistanceoftheDMRstothenearby gene?Allthesecriteriawillhavedramaticconsequences onthenumberandrobustnessof DMRsthatareidenti- fied, as well as the identification of DMR-associated genes and thus onthe interpretation on the results. In a complementary study, Yong-Villalobos et al. reported that differential methylation near Pi-responsive motif sequencesinthegenomecorrelateswithgeneexpression modulation, suggesting that the methylation status of someregulatoryelementscouldaffectthebindingcapac- ityofthecognatetranscriptionfactorsandhencecontrol

transcription[44].Suchamechanismhasbeenreportedin tomato fruit development, where the binding sites for RIN (Ripening Inhibitor), one the main transcription factors involved in fruit ripening, were frequently demethylatedduringripening,thus enablingtheinduc- tion of ripening genes [45]. Using a high-throughput approach, ithas recently been shown that>75% of the 327ArabidopsisTFssurveyedweremethylationsensitive [46],highlightingtheimportanceofDNAmethylationin modulating transcription factor binding. Recently, an additionalstudyreportedtheinvolvementofDNAmeth- ylation in controlling nutrient homeostasis, with the identification of the more sulphur accumulation1 (msa1) mutant, characterized by high sulphur levels in theshoots[47].MSA1isrequiredforthebiosynthesisof S-adenosylmethionine (SAM), which is a universal methyldonorformanymethylation reactions,including DNAmethylation.Asaconsequence,mutationinMSA1 resultedinaglobalreductionofDNAmethylationlevels, including localized changes at key sulphate responsive genes,suchasthetwohigh-affinitysulphatetransporter genesSULTR1;1and SULTR1;2[47].Furtheranalysis revealedthattheflankingsequenceof theS responsive element (SURE) of theSULTR1;1 promoter sequence, whichisessentialfortheSdeficiencyresponse,washypo- methylated inmsa1-1 roots. Such anobservation [47], withthatof Yong-Villalobosetal. [44],pointstowardsa keyroleofDNAmethylationinmodulatingtranscription factorbindingand/oroccupancytocontroltheexpression of key nutrient stress-responsive genes under specific stressconditions(Figure1).

Conclusionsand perspectives

Todate,multiplelinesofevidenceindicatethatchroma- tin remodelling is involved in controlling responses of plant to nutritional stresses and environmental cues in general.However,wearestillfarfromunderstandingthe underlying molecular mechanisms and significance of suchmodifications.Integrativestudiesassessingmultiple chromatin marks are still often missing, despite poten- tiallyprovidingkey informationonthecomplexregula- torymechanismsinvolvedintheseprocesses.Inaddition, therelationshipbetweentranscriptionalactivityandchro- matinmodificationsisoftenbasedoncorrelativestudies, andmoreeffortsarestillrequiredtoreliablyestablishthe causalityof theseprocesses.Similarly, to date,only sel- dom studieshave assessed thestability of these stress- induced changes in chromatin and how these marks wouldpotentiallycontributeto primingor trans-genera- tionalstressmemory.ThereductioninthepriceofDNA sequencingtechnologieswillhopefullycircumventthese current limitations. Furthermore, recent technological developments now enable the generation of cell type- specificor singlecelldatathatwillgreatly facilitatethe interpretationof these changesin chromatinmarks and their role in transcriptional regulation in response to nutritional stresses. The increase in the generation of

4 Cellsignallingandgeneregulation

largechromatinmarksdatasets,suchasDNAmethylation profiles,alsoraisesthecrucialneedtodefineaconsensus for definingDMRs,DMCsandotherparametersassoci- atedtoDNAmethylationprofilinganalysisthatcanaffect datainterpretation.Itisalsoimportant tokeepin mind thatmostofthestudiesperformedinthisfieldhavebeen undertaken in Arabidopsis, characterized by its small genome and relatively small population of transposable elementscomparedtootherplants,whichcouldaffectour current knowledge when transferred to agronomically important crops.Notably, oneofthebiggestchallenges for (epi)-genomics research in crops plants resides in generating and assembling accurate and representative genomes,oftencomplicatedbytheirlargegenomesizes, high proportion of related repeat sequences, and the closely related homeologous genes in polyploid crops.

Itisthuscrucialthatgenomicandbioinformaticapplica- tions are further developed to enable high-throughput identificationofnutrient-stressinducedchangesinchro- matin structure in crops.Understandingthe underlying mechanismswouldpotentiallyallowgenerationofstress- resilientplantsusingtherecentlydiscoveredtechniques for precisionepigenomeengineering.

Acknowledgements

Weapologizeforthemanyimportantstudiesthatwerenotcitedinthis reviewbecauseofspacelimitations.Thisworkwassupportedbythe AustralianResearchCouncilDECRAFellowship(DE150100460toDS) andbytheAustralianResearchCouncilCentreofExcellenceProgram (CE140100008toJWandRL).

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Normal Condition (eg+P)

Stress condition (eg-P)

TF

TF Pol

OFF

ON

RNA synthesis

Promoter

Promoter Stress inducible gene

Stress inducible gene

BSTF

TFBS

F TF

O TF

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