Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana.docVIP

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Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana.doc

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Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana

vanDijketal.BMCPlantBiology2010,10:238 /1471-2229/10/238 RESEARCH ARTICLE OpenAccess Dynamicchangesingenome-widehistone H3lysine4methylationpatternsinresponse todehydrationstressinArabidopsisthaliana KarinvanDijk1,5,YongDing1,SridharMalkaram1,Jean-JackMRiethoven1,2,RongLiu1,6,JingyiYang1,7, PeterLaczko1,HanChen1,YuannanXia1,IstvanLadunga1,3,ZoyaAvramova2,MichaelFromm1,4* Abstract Background:Themolecularmechanismsofgenomereprogrammingduringtranscriptionalresponsestostressare associatedwithspecificchromatinmodifications.Availabledata,however,describehistonemodificationsonlyat individualplantgenesinducedbystress.Wehavenoknowledgeofchromatinmodificationstakingplaceatgenes whosetranscriptionhasbeendown-regulatedoronthegenome-widechromatinmodificationpatternsthatoccur duringtheplant’sresponsetodehydrationstress. Results:Usingchromatinimmunoprecipitationanddeepsequencing(ChIP-Seq)weestablishedthewhole- genomedistributionpatternsofhistoneH3lysine4mono-,di-,andtri-methylation(H3K4me1,H3K4me2,and H3K4me3,respectively)inArabidopsisthalianaduringwateredanddehydrationstressconditions.Incontrasttothe relativelyevendistributionofH3throughoutthegenome,theH3K4me1,H3K4me2,andH3K4me3marksare predominantlylocatedongenes.About90%ofannotatedgenescarryoneormoreoftheH3K4methylation marks.TheH3K4me1andH3K4me2marksaremorewidelydistributed(80%and84%,respectively)thanthe H3K4me3marks(62%),buttheH3K4me2andH3K4me1levelschangedonlymodestlyduringdehydrationstress. Bycontrast,theH3K4me3abundancechangedrobustlywhentranscriptslevelsfromrespondinggenesincreased ordecreased.IncontrasttotheprominentH3K4me3peakspresentatthe5’-endsofmosttranscribedgenes, genesinduciblebydehydrationandABAdisplayedatypicallybroaderH3K4me3distributionprofilesthatwere presentbeforeandafterthestress. Conclusions:Ahighernumber(90%)ofannotatedArabidopsisgenescarryoneormoretypesofH3K4memarks thanpreviouslyreported.DuringtheresponsetodehydrationstressthechangesinH3K4me1,H3K4me2,and H3K4me3patternsshowdifferentdynamicsandspecifi