Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray 英文参考文献.docVIP

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Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray 英文参考文献.doc

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Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray 英文参考文献

Ratio-BasedAnalysisofDifferentialmRNAProcessing andExpressionofaPolyadenylationFactorMutantpcfs4 UsingArabidopsisTilingMicroarray JiantiZheng1,2.,DenghuiXing2.,XiaohuiWu1,2,YingjiaShen2,DianaM.Kroll2,GuoliJi1* ,Qingshun QuinnLi1,2 * 1DepartmentofAutomation,XiamenUniversity,Xiamen,Fujian,China,2DepartmentofBotany,MiamiUniversity,Oxford,Ohio,UnitedStatesofAmerica Abstract Background: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recentyears.ArabidopsispolyadenylationfactorPCFS4wasshowntofunctioninleafdevelopmentandinfloweringtime control.ThefunctionofPCFS4incontrollingfloweringtimewascorrelatedwiththealternativepolyadenylationofFCA ,a floweringtimeregulator.However,geneticevidencesuggestedadditionaltargetsofPCFS4thatmaymediateitsfunctionin bothfloweringtimeandleafdevelopment. Methodology/PrincipalFindings:Toidentifyfurthertargets,weinvestigatedthewholetranscriptomeofaPCFS4mutant usingAffymetrixArabidopsisgenomictiling1.0Rarrayanddevelopedadataanalysispipeline,termedRADPRE(Ratio-based AnalysisofDifferentialmRNAProcessingandExpression).InRADPRE,ratiosofnormalizedprobeintensitiesbetweenwild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data— variationscausedbydifferentialprobeaffinity—wassignificantlyalleviated.Withtheproberatiosasinputs,ahierarchyof statisticaltestswascarriedouttoidentifydifferentiallyprocessedgenes(DPG)anddifferentiallyexpressedgenes(DEG).The falsediscoveryrate(FDR)ofthisanalysiswasestimatedbyusingthebalancedrandomcombinationsofCol/pcfs4andpcfs4/ Col ratiosasinputs. Gene Ontology(GO) analysisof theDPGsandDEGs revealedpotential newrolesofPCFS4 instress responsesbesidesfloweringtimeregulation. Conclusion/Significance:Weidentified68DPGsand114DEGswithFDRat1%and2%,respectively.Mostofthe68DPGs weresubjectedtoalternativepolyadenylation,splicingortranscriptioninitiation.QuantitativePCRanalysisofasetofDPGs confirmed that most of these ge