Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites 英文参考文献.docVIP

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Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites 英文参考文献.doc

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Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites 英文参考文献

QuantitativeTestoftheBarrierNucleosomeModelfor StatisticalPositioningofNucleosomesUp-and DownstreamofTranscriptionStartSites WolframMo¨bius,UlrichGerland* ArnoldSommerfeldCenterforTheoreticalPhysicsandCenterforNanoScience,Ludwig-MaximiliansUniversita¨t Mu¨nchen,Munich,Germany Abstract ThepositionsofnucleosomesineukaryoticgenomesdeterminewhichpartsoftheDNAsequencearereadilyaccessiblefor regulatoryproteinsandwhicharenot.Genome-widemapsofnucleosomepositionshaverevealedasalientpatternaround transcriptionstartsites,involvinganucleosome-freeregion(NFR)flankedbyapronouncedperiodicpatternintheaverage nucleosomedensity.Whiletheperiodicpatternclearlyreflectswell-positionednucleosomes,thepositioningmechanismis lessclear.ArecentexperimentalstudybyMavrichetal.arguedthatthepatternobservedinSaccharomycescerevisiaeis qualitatively consistent with a ‘‘barrier nucleosome model,’’ in which the oscillatory pattern is created by the statistical positioningmechanismofKornbergandStryer.Ontheotherhand,thereisclearevidenceforintrinsicsequencepreferences ofnucleosomes,anditisuncleartowhatextentthesesequencepreferencesaffecttheobservedpattern.Totestthebarrier nucleosomemodel,wequantitativelyanalyzeyeastnucleosomepositioningdatabothup-anddownstreamfromNFRs.Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interactionofnucleosomesandtheirpositionalentropy.Wefindthatalthoughthetypicalpatternsonthetwosidesofthe NFR are different, they are both quantitatively described by the same physical model with the same parameters, but differentboundaryconditions.Theinferredboundaryconditionssuggestthatthefirstnucleosomedownstreamfromthe NFR(the+1nucleosome)istypicallydirectlypositionedwhilethefirstnucleosomeupstreamisstatisticallypositionedviaa nucleosome-repellingDNAregion.Theseboundaryconditions,whichcanbelocallyencodedintothegenomesequence, significantlyshapethestatisticaldistributionofnucleosomesoverarangeofupto,1,000bptoeach