Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data 英文参考文献.docVIP

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Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data 英文参考文献.doc

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Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data 英文参考文献

FeaturesofMammalianmicroRNAPromotersEmerge fromPolymeraseIIChromatinImmunoprecipitationData DavidL.Corcoran1.¤,KusumV.Pandit1,2.,BenGordon3,ArindamBhattacharjee3,NaftaliKaminski2*, PanayiotisV.Benos4,5 * 1DepartmentofHumanGenetics,GraduateSchoolofPublicHealth,UniversityofPittsburgh,Pittsburgh,Pennsylvania,UnitedStatesofAmerica,2DorothyP.andRichard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,UnitedStatesofAmerica,3Genomics,AgilentTechnologies,Inc.,SantaClara,California,UnitedStatesofAmerica,4DepartmentofComputationalBiology, UniversityofPittsburghSchoolofMedicine,Pittsburg,Pennsylvania,UnitedStatesofAmerica,5DepartmentofBiomedicalInformatics,UniversityofPittsburghSchoolof Medicine,Pittsburg,Pennsylvania,UnitedStatesofAmerica Abstract Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very importantroleindiversebiologicalprocessesandvariousdiseases.ManyalgorithmsareabletopredictmiRNAgenesand theirtargets, but theirtranscription regulation is stillunderinvestigation. Itis generally believedthatintragenic miRNAs (locatedinintronsorexonsofproteincodinggenes)areco-transcribedwiththeirhostgenesandmostintergenicmiRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoterorganizationiscurrentlyunknown. Methodology:WeperformedPolIIchromatinimmunoprecipitation(ChIP)-chipusingacustomarraysurroundingregionsof knownmiRNAgenes.ToidentifythetruecoretranscriptionstartsitesofthemiRNAgeneswedevelopedanewtool(CPPP). WeshowedthatmiRNAgenescanbetranscribedfrompromoterslocatedseveralkilobasesawayandthattheirpromoters sharethesamegeneralfeaturesasthoseofproteincodinggenes.Finally,wefoundevidencethatasmanyas26%ofthe intragenicmiRNAsmaybetranscribedfromtheirownuniquepromoters. Conclusion:miRNApromotershavesimilarfeaturestothoseofprot