Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins 英文参考文献.docVIP

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Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins 英文参考文献.doc

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Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins 英文参考文献

LeRoyetal.GenomeBiology2012,13:R68 /2012/13/8/R68 RESEARCH OpenAccess Proteogenomiccharacterizationandmappingof nucleosomesdecodedbyBrdandHP1proteins GaryLeRoy1?,IouriChepelev2?,PeterADiMaggio1,MarioABlanco1,BarryMZee1,3,KejiZhao2and BenjaminAGarcia1,3,4,5* Abstract Background:Histonepost-translationalmodifications(PTMs)constituteabranchofepigeneticmechanismsthat cancontroltheexpressionofeukaryoticgenesinaheritablemanner.RecentstudieshaveidentifiedseveralPTM- bindingproteinscontainingdiversespecializeddomainswhoserecognitionofspecificPTMsitesleadstogene activationorrepression.Here,wepresentahigh-throughputproteogenomicplatformdesignedtocharacterizethe nucleosomalmake-upofchromatinenrichedwithasetofhistonePTMbindingproteinsknownashistonePTM readers.WesupportourfindingswithgeneexpressiondatacorrelatingtoPTMdistribution. Results:Weisolatedhumanmononucleosomesboundbythebromodomain-containingproteinsBrd2,Brd3and Brd4,andbythechromodomain-containingheterochromatinproteinsHP1bandHP1a.HistonePTMswere quantifiedbymassspectrometry(ChIP-qMS),andtheirassociatedDNAsweremappedusingdeepsequencing.Our resultsrevealthatBrd-andHP1-boundnucleosomesareenrichedinhistonePTMsconsistentwithactively transcribedeuchromatinandsilentheterochromatin,respectively.DatacollectedusingRNA-SeqshowthatBrd- boundsitescorrelatewithhighlyexpressedgenes.Inparticular,Brd3andBrd4aremostenrichedonnucleosomes locatedwithinHOXgeneclusters,whoseexpressionisreduceduponBrd4depletionbyshorthairpinRNA. Conclusions:ProteogenomicmappingofhistonePTMreaders,alongsidethecharacterizationoftheirlocal chromatinenvironmentsandtranscriptionalinformation,shouldproveusefulfordetermininghowhistonePTMs areboundbythesereadersandhowtheycontributetodistincttranscriptionalstates. Background theformationandspreadingofconstitutiveheterochro- Acell’stranscriptional programisgovernednotonlyby matinandsilencingofeuchromatin.Incontrasttomethy- cis-actingDNAsequences,butalsobychromatinstructure, lation, histone H3 and H4 acetylat