Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation 英文参考文献.docVIP

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Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation 英文参考文献.doc

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Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation 英文参考文献

MutationsofDifferentMolecularOriginsExhibit ContrastingPatternsofRegionalSubstitutionRate Variation NavinElango1.,Seong-HoKim1.¤,NISCComparativeSequencingProgram2,EricVigoda3,SoojinV.Yi1* 1SchoolofBiology,GeorgiaInstituteofTechnology,Atlanta,Georgia,UnitedStatesofAmerica,2GenomeTechnologyBranchandNIHIntramuralSequencingCenter, NationalHumanGenomeResearchInstitute,NationalInstitutesofHealth,Bethesda,Maryland,UnitedStatesofAmerica, 3CollegeofComputing,GeorgiaInstituteof Technology,Atlanta,Georgia,UnitedStatesofAmerica Abstract TransitionsatCpGdinucleotides,referredtoas‘‘CpGsubstitutions’’,areamajormutationalinputintovertebrategenomes andaleadingcauseofhumangeneticdisease.TheprevalenceofCpGsubstitutionsisduetotheirmutationalorigin,which isdependentonDNAmethylation.Incomparison,othersinglenucleotidesubstitutions(forexamplethoseoccurringatGpC dinucleotides)mainlyarisefromerrorsduringDNAreplication.HereweanalyzedhighqualityBAC-baseddatafromhuman, chimpanzee,andbaboontoinvestigateregionalvariationofCpGsubstitutionrates. WeshowthatCpGsubstitutionsoccur approximately 15 times more frequently than other single nucleotide substitutions in primate genomes, and that they exhibitsubstantialregionalvariation.PatternsofCpGratevariationareconsistentwithdifferencesinmethylationleveland susceptibilitytosubsequentdeamination.Inparticular,weproposea‘‘distance-decaying’’hypothesis,positingthatdueto themolecularmechanismofaCpGsubstitution,ratesarecorrelatedwiththestabilityofdouble-strandedDNAsurrounding each CpG dinucleotide, and the effect of local DNA stability may decrease with distance from the CpG dinucleotide. Consistent with our ‘‘distance-decaying’’ hypothesis, rates of CpG substitution are strongly (negatively) correlated with regional G+C content. The influence of G+C content decays as the distance from the target CpG site increases.WeestimatethattheinfluenceoflocalG+Ccontentextendsupto1,500,2,000bpscenteredoneachCpGsite. We also show that the distance-decayi