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CARATTERIZZAZIONEFUNZIONALEDITRASCRITTIATTRAVERSOLINDIVIDUAZIONEDIELEMENTIDICONTROLLOPOSTTRASCRIZIONALEGRAZIANOPESOLEUNIVERSITDIMILANO7MARZO2002GRAZIANOPESOLEUNIMIITMICROARRAYEXPERIMENTRESULTGENECHARACTERIZATIONPROBLEMGENECLASSIFICATIONPROBLEMGENECHARACTERIZATIONPROBLEMESTSMRNA533CDSKNOWNGENEGENEIDENTIFICATIONTHROUGHDATABASESEARCHINGEGBLASTXGENEIDENTIFICATIONBYAAPATTERNDISCOVERYEGPFAM,ETCGENEIDENTIFICATIONBYNTPATTERNDISCOVERYEGUTRSITEPATTERNSESTASSEMBLINGGENECHARACTERIZATIONPROBLEMMRNA53CDSCDSDNAPROTEINEVENTUALALTERNATIVELYSPLICEDMRNASGENECHARACTERIZATIONPROBLEM3EST53CDSMRNA3UTRPOSTTRANSCRIPTIONALREGULATIONOFGENEEXPRESSIONSTABILITYTRANSLATIONSUBCELLULARLOCALIZATIONCDS3UTR5UTRMRNABIOLOGICALROLEOFMRNAUTRSNUCLEAREXPORTPOLYADENYLATIONSTATUSMRNACELLULARLOCALIZATIONCONTROLOFMRNASTABILITYCONTROLOFMRNATRANSLATIONFUNCTIONMEDIATEDBYOLIGONUCLEOTIDEPATTERNSSTEMLOOPSTRUCTURESPATTERNSKNOWNTOPLAYSOMEREGULATORYACTIVITYEXPERIMENTALASSAY,PHYLOGENETICFOOTPRINTINGNOVELPATTERNSCANDIDATEOFFUNCTIONALACTIVITYSTATISTICALANALYSESCARRIEDOUTONNONREDUNDANTDATABASESUTRDBRELEASE140JANUARY2001FUNCTIONALELEMENTSANNOTATIONUTRSITEDATABASECONSENSUSOLIGONUCLEOTIDESCONSENSUSSECONDARYSTRUCTURESREGULAREXPRESSIONSTRINGSCONSENSUSMATRICESEGAAUAAAPOLYADENYLATIONSITECX2,4CX3LIVMFYWCX8HX3,5HC2H2ZINCFINGERDETERMINISTICDESCRIPTIONOFTHEPATTERNYES/NOPROBABILISTICDESCRIPTIONOFTHEPATTERNTHRESHOLDVALUEAURICHELEMENTSARESAURICHELEMENTSARESPRESENTINTHE3UNTRANSLATEDREGIONOFMATURELYMPHOKINEANDCYTOKINEMRNASREGULATEMRNASTABILITYANDTRANSLATIONALEFFICIENCYBASEDONTHEIRSEQUENCEFEATURESANDFUNCTIONALPROPERTIESARESCANBEDIVIDEDINTOTHREECLASSESCLASSIIARESDIRECTASYNCHRONOUSCYTOPLASMICDEADENYLATIONPROCESSIVEKINETICSGENERATINGPOLYAMRNASAMONGMRNASWITHCLASSIIAREINTHEIR3UTRAREGMCSF,IL2THEMINIMUMNUMBEROFAUUUATANDEMMOTIFSTOACTIVATEPROCESSIVEDEGRADATIONIS4OFWHICHATLEAST3INTANDEMFURTHERMORE,ANAURICHREGION2030NTLONGIMMEDIATELY5TOTHECLUSTEROFAUUUAMOTIFSCANGREATLYENHANCETHEDEGRADATIONACTIVITYCDSAURICHAN5UTR3UTRAREIIAUUUACYTOPLASMICPOLYADENYLYLATIONCYTOPLASMICPOLYADENYLATIONISANEVOLUTIONARILYCONSERVEDMECHANISMREGULATINGTRANSLATIONALACTIVATIONOFASETOFQUIESCENTMATERNALMESSENGERRNASMRNASDURINGEARLYDEVELOPMENTCYTOPLASMICPOLYAELONGATIONOCCURSINAWIDERANGEOFSPECIES,RANGINGFROMCLAMTOMOUSETHERELEVANCEOFTHISPROCESSDURINGLATEOOGENESISANDEARLYEMBRYOGENESISHASBEENSHOWNBYSTUDIESINTHEMOUSE,XENOPUS,ANDDROSOPHILAINMOUSEANDXENOPUS,THEONLYVERTEBRATESSOFAREXAMINED,THECRITICALREGULATORYSEQUENCES,REFERREDTOASCYTOPLASMICPOLYADENYLATIONELEMENTSCPES,AREAURICHANDLOCATEDINTHE3UNTRANSLATEDREGION3UTRNEARTHECANONICALNUCLEARPOLYADENYLATIONELEMENTAAUAAA,WHICHALSOISREQUIREDFORPROPERPOLYAADDITIONTHECPEHASTHEGENERALSTRUCTUREOFUUUUUUAUHOWEVER,THECPEISNOTIDENTICALINALLMRNASANDITSPOSITIONVARIESRELATIVETOAAUAAAGENERALLYWITHIN100NUCLEOTIDESTHEMINIMALCPECAPABLETOSTIMULATEELONGATIONOFAPOLYATAILAPPEARSTOBEUUUUAU,ANDRECENTEXPERIMENTSSHOWALSOTHEEXISTENCEOFSUBSTANTIALCONTEXTANDPOSITIONEFFECTSONCPEFUNCTIONCDSUUUUUUAUAAUAAAAN5UTR3UTRCPEMRNAPATTERNSUSUALLYLOCATEDIN5OR3UTRSTHATAREABLETOFOLDINTOSPECIFICSECONDARYSTRUCTURESABLETOBERECOGNIZEDBYSPECIFICRNABINDINGPROTEINSHISTONE3UTRMRNAELEMENTMETAZOANHISTONE3UTRMRNAS,LACKINGAPOLYATAIL,CONTAINAHIGHLYCONSERVEDSTEMLOOPSTRUCTUREWITHASIXBASESTEMANDAFOURBASELOOPTHISSTEMLOOPSTRUCTUREPLAYSADIFFERENTROLEINTHENUCLEUSANDINTHECYTOPLASMINTHENUCLEUS,ITISINVOLVEDINPREMRNAPROCESSINGANDNUCLEOCYTOPLASMICTRANSPORT,WHEREASINTHECYTOPLASMITENHANCESTRANSLATIONEFFICIENCYANDREGULATESHISTONEMRNASTABILITYTHETRANSACTINGFACTORWHICHINTERACTSWITHTHE3UTRHAIRPINSTRUCTUREOFHISTONEMRNASISA31KDASTEMLOOPBINDINGPROTEININMAMMALSSLBPPRESENTBOTHINNUCLEIANDPOLYRIBOSOMESINMAMMALSINADDITIONTOSLBPHISTONEMRNAPROCESSINGREQUIRESATLEASTONEADDITIONALFACTORTHEU7SNRNP,WHICHBINDSAPURINERICHELEMENT1020NTDOWNSTREAMOFTHESTEMLOOPSEQUENCEHISTONEDOWNSTREAMELEMENT,HDETHEHISTONE3UTRHAIRPINSTRUCTUREISPECULIARINTHATTHEBASESOFTHESTEMARECONSERVEDUNLIKEMOSTFUNCTIONALHAIRPINMOTIFSWHERECONSERVEDBASESAREFOUNDINSINGLESTRANDEDLOOPREGIONSONLYTHESEQUENCEOFTHESTEMANFLANKINGSEQUENCESARECRITICALFORBINDINGOFTHESLBPSELENOCYSTEINEINSERTIONSEQUENCESECISSPECIFICINCORPORATIONOFSELENOCYSTEINEINSELENOPROTEINSISDIRECTEDBYUGACODONSRESIDINGWITHINTHECODINGSEQUENCEOFTHECORRESPONDINGMRNASTRANSLATIONOFUGA,USUALLYATERMINATIONCODON,ASSELENOCYSTEINEREQUIRESACONSERVEDSTEMLOOPSTRUCTURECALLED“SELENOCYSTEINEINSERTIONSEQUENCE“SECISLYINGINTHE3UTRREGIONOFSELENOPROTEINMRNASTHECONSENSUSSTRUCTUREOFSECISELEMENTDETERMINEDBYCOMPARATIVEANALYSISOFSEVERALSELENOPROTEINMRNASASWELLASONBOTHRNASEANDCHEMICALPROBINGUGASECISNANOSTCETHE3UTROFDROSOPHILANANOSMRNACONTAINSTHEESSENTIALSIGNALSFORGENERATINGTHENANOSGRADIENTEMANATINGFROMTHEPOSTERIORPOLEOFDROSOPHILAEMBRYOSTHEPOLARIZEDDISTRIBUTIONOFNANOSISGENERATEDBYTHELOCALIZATIONDEPENDENTTRANSLATIONOFNANOSMRNAINTHEPOLEPLASMTHETRANSLATIONCONTROLELEMENTTCECONSISTSOFAA90NTREGIONLOCATEDINTHE3UTROFNANOSMRNAWHICHISABLETOFOLDINTOABIPARTITESECONDARYSTRUCTURETHATISRECOGNIZEDBYSMAUGREPRESSORANDATLEASTONEADDITIONALFACTORASTEMLOOPBEARINGTHECUGGCPENTAMERINTHELOOPISREQUIREDFORSMAUGTCEINTERACTIONWHEREASBOTHSEQUENCEANDSTRUCTUREOFANOTHERSTEMLOOPISCRITICALFORTCEFUNCTIONTRANSLATIONACTIVATIONISMEDIATEDBYTHEINTERACTIONOFLOCALIZATIONFACTORSWITHA540NTSEQUENCEREGIONSOVERLAPPINGTHETCESTRUCTURALMOTIFLOCALIZATIONOFNANOSRNATOTHEPOSTERIORPOLEOFTHEEMBRYOISESSENTIALFORTRANSLATIONOFNANOSPROTEININSITUHYBRIDIZATIONTONANOSRNATOP,ANTIBODYSTAININGWITHANTINANOSANTIBODYBOTTOMPATSEARCHISAPATTERNMATCHERWHICHSEARCHESPROTEINORNUCLEOTIDEDNA,RNA,TRNA,ANDSOONSEQUENCESINORDERTOFINDINSTANCESOFAPATTERNWHICHYOUCANGIVEASINPUTITISABLETOFIND,INAGIVENSEQUENCE,KINDSOFLOOPSTRUCTURESTHATCHARACTERIZETRNAS,RRNASHAIRPINLOOP,STEMLOOPWITHBULGESORINTERNALLOOPSAND/ORANYKINDOFPATTERNINDNAANDPROTEINSEQUENCESPATSEARCHALSOALLOWSTOUSENONSTANDARDPAIRINGSFORREVERSEMATCHINGANDTOLERATESOMENUMBERSOFMISMATCHESANDBULGESAPATTERNISASEQUENCEOFSIMPLEPATTERNUNITSASIMPLEPATTERNUNITISEITHERANAMEDPATTERNUNIT,ACOMPLEMENTATIONRULEPATTERNUNITORABASICPATTERNUNITINPATTERNDEFINITION,UPPERANDLOWERCASECANBEUSEDINTERCHANGEABLYNAMEDPATTERNUNITNAMEBASICPATTERNP147ORP1ACGTAGTCOMPLEMENTATIONRULEPATTERNUNITNAMECOMPLEMENTSR1AU,UA,GC,CGBASICPATTERN1STRINGOFCHARACTERSTOBEMATCHEDINCLUDINGSTANDARDAMBIGUITYCODESFORNUCLEOTIDESANDCHARACTERXFORPROTEINS,OPTIONALLYFOLLOWEDBYAMATCHQUALIFIEROFTHEFORMMISMATCHES,DELETIONS,INSERTIONSEXAMPLETATAA1,0,0MATCHTATAA,ALLOWING1MISMATCH2RANGEPATTERNUNITOFTHEFORM“MINMAX”EXAMPLE05MATCH1TO5CHARACTERSORNONE3COMPLEMENTPATTERNUNITTHATISUSEDTOMATCHTHEREVERSECOMPLEMENTOFANAMEDPATTERNUNIT,PREVIOUSLYDEFINEDEXAMPLER1P2MATCHTHEREVERSECOMPLEMENTOFP2USINGRULESR14LENGTHLIMITPATTERNUNITPUTSAUPPERORLOWERBOUNDONTHESUMOFTHELENGTHSMATCHEDBYPREVIOUSNAMEDPATTERNUNITSEXAMPLELENGTHP1P2P395WEIGHTPATTERNUNITISUSEDFORMATCHINGAGAINSTNUCLEOTIDESEQUENCESBYUSINGAWEIGHTMATRIXLOGODDSSCORINGMETHODORMATRIXSIMILARITYMETHODHISTONE3UTRMRNAELEMENTPATSEARCHPATTERNR1AU,UA,GC,CG,GU,UGNMMMP1GGYYYUHHUHAR1P1MM03MA/CYC/UHNOTGAUGINTERNALRIBOSOMEENTRYSITEIRESPATSEARCHSYNTAXR1AU,UA,CG,GC,GU,UGP15606P256P302P458P538R1P41,0,0P658P735R1P61,0,0P805R1P21,0,006R1P11,0,025P956P1038R1P91,0,0310HTTP/BIGAREAAREABACNRIT8000/EMBIT/PATSEARCHHTMLEM_EST1AA545838420,442CCAACGGCCCTCTTTAGGGCCACEM_EST1AA545875369,391CCAACGGCCCTCTTTAGGGCCACEM_EST1AA545884419,441CCAACGGCCCTCTTTAGGGCCACEM_EST1AA563524422,444CCAACGGCCCTCTTTAGGGCCACEM_EST1AA610040403,425CCAAAGGCTCTTTTCAGAGCCACEM_EST2AA701695155,177CCAACGGCCCTCTTTAGGGCCACDATABASEDIVISIONENTRYNAMEPOSITIONMATCHEDPATTERNSEARCHOFTHEHISTONE3UTRMOTIFINESTSEQUENCESGIVENTHATONLYABOUTONERANDOMHITOFTHISPATTERNISEXPECTEDIN100MBWECANRELIABLYASSIGNTHEMATCHEDESTSTOMRNASCODINGFORHISTONERELATEDPROTEINSPATTERNSKNOWNTOPLAYSOMEREGULATORYACTIVITYEXPERIMENTALASSAY,PHYLOGENETICFOOTPRINTINGNOVELPATTERNSCANDIDATEOFFUNCTIONALACTIVITYSTATISTICALANALYSESCARRIEDOUTONNONREDUNDANTDATABASESMONITORINGGENEEXPRESSIONUSINGDNAMICROARRAYSASOMCLUSTERINGBHIERARCHICALCLUSTERINGIFYOUHAVEAGROUPOFGENESWITHASIMILAREXPRESSIONPROFILEEGTHOSEACTIVATEDATTHESAMETIMEINCELLCYCLEANATURALASSUMPTIONISTHATTHISPROFILEIS,ATLEASTPARTLY,CAUSEDBYANDREFLECTEDINASIMILARSTRUCTUREOFREGIONSINVOLVEDINTRANSCRIPTIONREGULATIONRESEARCHHASTHUSFOCUSEDONTHEDETECTIONOFMOTIFSPOSSIBLYREPRESENTINGTFBINDIINGSITESCOMMONTOTHEPROMOTERSEQUENCESOFPUTATIVELYCOREGULATEDGENESSIGNIFICANTPATTERNRANDOMPATTERNVOCCURRENCEVPOSITIONVINFORMATIONCONTENTVOCCURRENCETHENUMBEROFSEQUENCESCONTAININGAGIVENPATTERNSHOULDBESIGNIFICANTLYGREATERTHANEXPECTEDEGWORDUPALGORITHMPATTERNSOBSERVEDEXPECTEDCHISQUAREAATAAA134541400035209362225AAATAA8344140003542608588ATAAAG5782581292839637997ATAAAA7444140003526304270CCCCCC2736546104722246291ATAAAT5843212229121496537GAAATA4432391449817377269TAAATA4962854436215531610TGTATTT2431031833318945602TGTATAT154563408316927891ATATTTA221952544516599689TTTATAT2181038743212538875TGTACAT130504865012522942ATATATA136590811910014193GCGGCCGC3854152719606842ATATATTT100314202414968643GGGTGGGG92318225111379774TTTAAAAA2111038944411041593TACATTTT92334071110276638TATTTATTT94166026936080574TTTTTAAAA139402507724226645VPOSITIONFUNCTIONALPATTERNSAREGENERALLYINCONSERVEDPOSITIONSEGWITHINASPECIFICDISTANCERANGEFROMTHETRANSCRIPTIONSTARTSITEVINFORMATIONCONTENTTHEFUNCTIONALCONSTRAINTSONEACHSPECIFICPOSITIONOFTHEPATTERNAREVARIABLEFROMSOMESITESABSOLUTELYCONSERVEDSHANNONSINFORMATIONCONTENTCIRANGINGBETWEEN0AND1TENRANDOMSEQUENCES1KBLONG,EACHCONTAININGTHESAME15MERMOTIFUPTO2MISMATCHESALLOWEDTWODIFFERENTAPPROACHESCANBEUSEDTOEXTRACTFUNCTIONALMOTIFSFROMREGULATORYREGIONSOFCOREGULATEDGENESVALIGNMENTMETHODSVENUMERATIONOREXAUSTIVEMETHODSTRYTOIDENTIFYUNKNOWNSIGNALSBYASIGNIFICANTLOCALMULTIPLEALIGNMENTOFALLSEQUENCESVGIBBSSAMPLINGVMEMESYSTEMEXPECTATIONMAXIMIZATIONTHESEMETHODSUSEASTATISTICALAPPROACHTHATCONSIDERSUNKNOWNTHESTARTPOSITIONOFTHEMOTIFSINTHESEQUENCESANDPERFORMALOCALOPTIMIZATIONTODETERMINEWHICHPOSITIONSDELIVERTHE“OPTIMAL”MOTIFSTWOAPPROACHESSITESAMPLINGEACHSEQUENCEISASSUMEDTOCONTAINONEMOTIFELEMENTFOREACHMOTIFTYPEMOTIFSAMPLINGEACHSEQUENCEISASSUMEDTOCONTAINONEMOTIFELEMENTFOREACHMOTIFTYPEHTTP/BAYESWEBWADSWORTHORG/GIBBS/GIBBSHTMLHTTP/MEMESDSCEDU/MEME/WEBSITE/VWORDUPHTTP/BIOWWWBACNRIT8000/BIOWWW/WORDUPGCGHTMLVYEBISHTTP/WWWSCCJSTGOJP8080/SANKICHI/MOTIFEXTRACTION/VPRATTHTTP/WWWIIUIBNO/INGE/PRATTHTML/VVERBUMCULUSHTTP/WWWCSPURDUEEDU/HOMES/STELO/VERBUMCULUS/VRSATOOLSHTTP/COPANCIFNUNAMMX/JVANHELD/RSATOOLS/TESTDATASET20SEQUENCES100NTLONGWITHA8MERSHAREDBY75OFTHEMOCCURRENCESWORDSOBSERVEDEXPECTEDCHISQUAREGGATCA1505836151GATCAA1506332596ATCAAA1506531696AGGATC70577270TGGATC60486310TCAAAG70666058GTGGAT40452805GCAAGC50692700GTTTGG40492509CAAAGT40562122OCCURRENCESWORDSOBSERVEDEXPECTEDCHISQUAREAGGATC70577270GCAAGC50692700GTTTGG40492509TCAAAGT40

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