Small RNAs Originated from Pseudogenes cis- or trans-Acting 英文参考文献.docVIP

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Small RNAs Originated from Pseudogenes cis- or trans-Acting 英文参考文献.doc

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Small RNAs Originated from Pseudogenes cis- or trans-Acting 英文参考文献

SmallRNAsOriginatedfromPseudogenes:cis-ortrans- Acting? XingyiGuo1,ZhaoleiZhang2,MarkB.Gerstein3,DeyouZheng1,4* 1InstituteforBrainDisordersandNeuralRegeneration,DepartmentofNeurology,AlbertEinsteinCollegeofMedicine,NewYork,NewYork,UnitedStatesofAmerica, 2Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, 3Department of Molecular Biophysics and Biochemistry,YaleUniversity,NewHaven,Connecticut,UnitedStatesofAmerica,4DepartmentofGeneticsandDepartmentofNeuroscience,AlbertEinsteinCollegeof Medicine,NewYork,NewYork,UnitedStatesofAmerica Abstract Pseudogenesaresignificantcomponentsofeukaryoticgenomes,andsomehaveacquirednovelregulatoryroles.Todate, nostudyhascharacterizedricepseudogenessystematicallyoraddressedtheirimpactonthestructureandfunctionofthe rice genome. In this genome-wide study, we have identified 11,956 non-transposon-related rice pseudogenes, most of whicharefromgeneduplications.About12%ofthericeprotein-codinggenes,halfofwhichareinsingletonfamilies,have apseudogeneparalog.Interestingly,wefoundthat145ofthesepseudogenespotentiallygaverisetoantisensesmallRNAs afterexamining,1.5millionsmallRNAsfromdevelopingricegrains.Themajority(.50%)oftheseantisenseRNAsare24- nucleotides long, a feature often seen in plant repeat-associated small interfering RNAs (siRNAs) produced by RNA- dependentRNApolymerase(RDR2)andDicer-likeprotein3(DCL3),suggestingthatsomepseudogene-derivedsiRNAsmay be implicated in repressing pseudogene transcription (i.e., cis-acting). Multiple lines of evidence, however, indicate that small RNAs from rice pseudogenes might also function as natural antisense siRNAs either by interacting with the complementarysenseRNAsfromfunctionalparentalgenes(38cases)orbyformingdouble-strandRNAswithtranscriptsof adjacentparalogous pseudogenes(2cases)(i.e., trans-acting). Further examinationsoffiveadditionalsmall RNAlibraries revealed that pseudogene-derived antisense siRNAs could be produced in specifi