PARalyzer definition of RNA binding sites from PAR-CLIP short-read sequence data 英文参考文献.docVIP

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PARalyzer definition of RNA binding sites from PAR-CLIP short-read sequence data 英文参考文献.doc

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PARalyzer definition of RNA binding sites from PAR-CLIP short-read sequence data 英文参考文献

Corcoranetal.GenomeBiology2011,12:R79 /2011/12/8/R79 METHOD OpenAccess PARalyzer:definitionofRNAbindingsitesfrom PAR-CLIPshort-readsequencedata DavidLCorcoran1?,StoyanGeorgiev1,2?,NeelanjanMukherjee1,EvaGottwein3,4,RebeccaLSkalsky5, JackDKeene5andUweOhler1,6* Abstract Crosslinkingandimmunoprecipitation(CLIP)protocolshavemadeitpossibletoidentifytranscriptome-wideRNA- proteininteractionsites.Inparticular,PAR-CLIPutilizesaphotoactivatablenucleosideformoreefficientcrosslinking. Wepresentanapproach,centeredonthenovelPARalyzertool,formappinghigh-confidencesitesfromPAR-CLIP deep-sequencingdata.WeshowthatPARalyzerdelineatessiteswithahighsignal-to-noiseratio.Motiffinding identifiesthesequencepreferencesofRNA-bindingproteins,aswellasseed-matchesforhighlyexpressed microRNAswhenprofilingArgonauteproteins.Ourstudydescribestailoredanalyticalmethodsandprovides guidelinesforfutureeffortstoutilizehigh-throughputsequencinginRNAbiology.PARalyzerisavailableathttp:// /labs/ohler/research/PARalyzer/. Background RNA-proteininteractionsoccurwithinatranscript.The RNAbindingproteins(RBPs)playimportantrolesinthe second method, CLIP, typically uses short wave UV lifecycleofatranscript,fromitsnascencebyRNApoly- 254nmcrosslinkingfollowedbyimmunoprecipitationand meraseuntilitsdecaybyRNases.AllstepsofRNAproces- partialRNasedigestionoftheboundtranscript.Conver- sing and function, including splicing, nuclear export, sionoftheresidual RNAsegmentsintocDNAlibraries localization,stability,andsmallRNA-mediatedregulation, andcharacterizationbyhigh-throughputsequencingyields arecontrolledbydifferentRBPsandribonucleoproteins smallsizewindowsinwhichtheRNA-proteincrosslinking [1].Theidentification ofwhichRBPsorribonucleopro- teinsinteract withwhichtranscripts, howtheyinteract, occurred. PAR-CLIP(photoactivatable-ribonucleoside-enhanced andwheretheinteraction occurs,hasbeenthefocusof crosslinkingandimmunoprecipitation)isapowerfulmod- manystudies.Recentadvancementsinhigh-thro