Pseudo–Messenger RNA Phantoms of the Transcriptome 英文参考文献.docVIP

Pseudo–MessengerRNA:Phantoms oftheTranscriptome Martin C.Frith1,2,Laurens G.Wilming3,Alistair Forrest2,Hideya Kawaji1,Sin Lam Tan4,5,Claes Wahlestedt6,7 , Vladimir B.Bajic4,5,Chikatoshi Kai1,Jun Kawai1,8,Piero Carninci1,8,Yoshihide Hayashizaki1,8,Timothy L.Bailey2, Lukasz Huminiecki6,9* 1GenomeExplorationResearchGroup(GenomeNetworkProjectCoreGroup),RIKENGenomicSciencesCenter,RIKENYokohamaInstitute,Yokohama,Japan,2Institutefor Molecular Bioscience, University of Queensland, Brisbane, Australia, 3 Wellcome Trust Sanger Institute, Hinxton, United Kingdom, 4 Institute for Infocomm Research, Singapore,Singapore,5UniversityoftheWesternCape,SouthAfricanNationalBioinformaticsInstitute,Bellville,SouthAfrica,6CenterforGenomicsandBioinformatics, KarolinskaInstitutet,Stockholm,Sweden,7DepartmentofBiomedicalSciences,TheScrippsResearchInstitute,Jupiter,Florida,UnitedStatesofAmerica,8GenomeScience Laboratory,DiscoveryResearchInstitute,RIKENWakoInstitute,Wako,Japan,9LudwigInstituteforCancerResearch,UppsalaUniversitet,Uppsala,Sweden The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes,wedefinepseudo–messengerRNAtobeRNAmoleculesthatresembleprotein-codingmRNA,butcannot encodefull-lengthproteinsowingtodisruptionsofthereadingframe.Usingarigorouscomputationalpipeline,which rulesoutsequencingerrors,weidentify10,679pseudo–messengerRNAs(approximatelyhalfofwhicharetransposon- associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein-coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense-mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteinsthancurrentlyestimated.Wealsodescribecompensatoryframeshifts,whereasegmentofthegenehas changed frame but