Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers 英文参考文献.docVIP

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Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers 英文参考文献.doc

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Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers 英文参考文献

Wilsonetal.GigaScience2012,1:3 /content/1/1/3 RESEARCH OpenAccess Resourcesformethylomeanalysissuitablefor geneknockoutstudiesofpotential epigenomemodifiers GarethAWilson1*,PawandeepDhami1,AndrewFeber1,DanielCortázar2,YukaSuzuki1,ReinerSchulz3, PrimoSch?r2andStephanBeck1* Abstract Background:MethylatedDNAimmunoprecipitation(MeDIP)isapopularenrichmentbasedmethodandcanbe combinedwithsequencing(termedMeDIP-seq)tointerrogatethemethylationstatusofcytosinesacrossentire genomes.However,qualitycontrolandanalysisofMeDIP-seqdatahaveremainedtobeachallenge. Results:Wereportgenome-wideDNAmethylationprofilesofwildtype(wt)andmutantmousecells,comprising3 biologicalreplicatesofThymineDNAglycosylase(Tdg)knockout(KO)embryonicstemcells(ESCs),invitro differentiatedneuralprecursorcells(NPCs)andembryonicfibroblasts(MEFs).Theresulting18methylomeswere analysedwithMeDUSA(MethylatedDNAUtilityforSequenceAnalysis),anovelMeDIP-seqcomputationalanalysis pipelinefortheidentificationofdifferentiallymethylatedregions(DMRs).Theobservedincreaseof hypermethylationinMEFpromoter-associatedCpGislandssupportsapreviouslyproposedroleforTdginthe protectionofregulatoryregionsfromepigeneticsilencing.Furtheranalysisofgenesandregionsassociatedwith theDMRsbygeneontology,pathway,andChIPanalysesrevealedfurtherinsightsintoTdgfunction,includingan associationofTDGwithlow-methylateddistalregulatoryregions. Conclusions:WedemonstratethatMeDUSAisabletodetectbothlarge-scalechangesbetweencellsfrom differentstagesofdifferentiationandalsosmallbutsignificantchangesbetweenthemethylomesofcellsthatonly differintheKOofasinglegene.Thesechangeswerevalidatedutilisingpubliclyavailabledatasetsandconfirm TDGsfunctionintheprotectionofregulatoryregionsfromepigeneticsilencing. Keywords:Methylome,MeDIP-seq,Epigenetics,Epigenomics,DNAmethylation,Computationalpipeline,MeDUSA Background In mammalian genomes, methylation predominantly DNAmethylationisanimportantepigeneticmodification, occurs symmetrically on both DNA strands at palin- playi