Transcriptome-widemiR-155bindingmaprevealswidespreadnon-canonicalmicroRNAtargetingGabrielB.Loeb1,*,AlyA.Khan2,3,*,DavidCanner1,JosephB.Hiatt4,JayShendure4,RobertB.Darnell5,ChristinaS.Leslie3,andAlexanderY.Rudensky1,#1HowardHughesMedicalInstituteandImmunologyProgram,MemorialSloan-KetteringCancerCenter,NewYork,NY10065,USA2InstituteforGenomicsandSystemsBiology,UniversityofChicago,Chicago,IL60637,USA3ComputationalBiologyProgram,MemorialSloan-KetteringCancerCenter,NewYork,NY10065,USA4DepartmentofGenomeSciences,UniversityofWashington,Seattle,WA98195,USA5HowardHughesMedicalInstitute,LaboratoryofMolecularNeuro-Oncology,TheRockefellerUniversity,NewYork,NY10065,USAAbstractmicroRNAs(miRNAs)areessentialcomponentsofgeneregulation,butidentificationofmiRNAtargetsremainsamajorchallenge.MosttargetpredictionanddiscoveryreliesonperfectcomplementarityofthemiRNAseedtothe3′untranslatedregion(UTR).However,itisuncleartowhatextentmiRNAstargetsiteswithoutseedmatches.Here,weperformedatranscriptome-wideidentificationoftheendogenoustargetsofasinglemiRNA—miR-155—inageneticallycontrolledmanner.WefoundthatapproximatelyfortypercentofmiR-155-dependentArgonautebindingoccursatsiteswithoutperfectseedmatches.Themajorityofthesenon-canonicalsitesfeatureextensivecomplementaritytothemiRNAseedwithonemismatch.Thesenon-canonicalsitesconferregulationofgeneexpressionalbeitlesspotentlythancanonicalsites.Thus,non-canonicalmiRNAbindingsitesarewidespread,oftencontainseed-likemotifs,andcanregulategeneexpression,generatingacontinuumoftargetingandregulation.IntroductionmiRNAsdirectArgonaute(AGO)proteinstopost-transcriptionallyrepressmessengerRNA(mRNA)targetsandregulateabroadrangeofphysiologicalprocesses(Ambros,2004;Bartel,2004,2009).WhilegainandlossoffunctionstudieshaveestablishedspecificrolesofindividualmiRNAs,theidentityofmostmiRNAtargetsremainsunknown,whichlimitsmechanisticinsightintoobservedphenotypes.Forinstance,itisunclearwhetherindividual©2012ElsevierInc.Allrightsreserved.#Correspondenceandrequestsformate...
