Repertoires of the Nucleosome-Positioning Dinucleotides 英文参考文献.docVIP

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Repertoires of the Nucleosome-Positioning Dinucleotides 英文参考文献.doc

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Repertoires of the Nucleosome-Positioning Dinucleotides 英文参考文献

RepertoiresoftheNucleosome-Positioning Dinucleotides ThomasBettecken1*,EdwardN.Trifonov2,3 1CAGT–CenterforAppliedGenotyping,MaxPlanckInstituteofPsychiatry,Munich,Germany,2GenomeDiversityCenter,InstituteofEvolution,UniversityofHaifa,Haifa, Israel,3DivisionofFunctionalGenomicsandProteomics,FacultyofScience,MasarykUniversity,Brno,CzechRepublic Abstract ItisgenerallyacceptedthattheorganizationofeukaryoticDNAintochromatinisstronglygovernedbyacodeinherentin thegenomicDNAsequence.Thiscode,aswellasothercodes,issuperposedonthetripletscodingforaminoacids.The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides,withAA/TTandRR/YYgivingthestrongestsignals,allwithaperiodof10.4bases.Everybase-pairstackinthe DNAduplexhasspecificdeformationproperties,thusfavoringDNAbendinginaspecificdirection.Theappearanceofthe correspondingdinucleotideatthedistance10.4xnbaseswillfacilitateDNAbendinginthatdirection,whichcorrespondsto theminimumenergyofDNAfoldinginthenucleosome.Wehaveanalyzedtheperiodicappearancesofall16dinucleotides inthegenomesofthirteendifferenteukaryoticorganisms.Ourdatashowthatalargevarietyofdinucleotides(ifnotall)are, apparently,contributingtothenucleosomepositioningcode.Thechoiceoftheperiodicaldinucleotidesdiffersconsiderably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observedforCGdinucleotidesinthegenomeofthehoneybeeA.mellifera.Also,thedinucleotideCGappearsastheonly periodical component in the human genome. This observation seems especially relevant since CpG methylation is well known to modulate chromatin packing and regularity. Thus, the selection of the dinucleotides contributing to the chromatincodeisspeciesspecific,andmaydifferfromregiontoregion,dependingonthesequencecontext. Citation:BetteckenT,TrifonovEN(2009)RepertoiresoftheNucleosome-PositioningDinucleotides.PLoSONE4(11):e7654.doi:10.1371/journal.pone.0007654 Editor:CathalSe