Non-coding RNA

Non-codingRNAWhatisnoncodingRNA?Non-codingRNA(ncRNA)isaRNAmoleculethatfunctionswithoutbeingtranslatedintoaproteinHowmanyRNAsincells?mRNArRNAtRNAProteinsnRNAsnoRNAgRNAAntisenseRNASRP-RNAmicroRNApRNARibozymeTelomeraseRNA??FunctionaldiversityofncRNAsSchemeforthefunctionofdifferentsncRNAsbytargetingbacterialoreukaryalmRNAsorpre-mRNAsleadingtoregulationofgeneexpressionThefunctionofdiffenentsmallnon-codingRNAsbytargetingmRNAsorpre-mRNAsnon-codingRNA(20-20000nt)RNAmRNAsmallnon-codingRNA(sncRNA)(20-500nt)longnon-codingRNA(lncRNA)(500-20000nt)Non-codingRNA:VersatilityinformandfunctionNoncodingRNAgenesaresurprisinglynumerous.NoncodingRNAhaveaverydifferentfunctions.TimeforRNomicsCell,89:669–672,May30,1997PNAS,97(26):14035-14037,Dec19,2000UnderstandingRNomicsfromanexpendingsnoRNAworldCouzinJ.Breakthroughoftheyear.SmallRNAsmakebigsplash.Science.2002Dec20;298(5602):2296-7.DNARNAProteinStudynon-codingRNAsonthegenomicscaleStudytheidentification,expression,biogenesis,structure,regulationofexpression,targets,andbiologicalfunctionsofnoncodingRNAsonthegenomicscale.sncRNAsareverysmallsncRNAscontainnospecificfeaturesattheir5’and3’endsHowtoidentifythencRNAgenesingenomicstudies?methodsforfindingnovelnon-codingRNAgenesComputationalRNomicsSearchingconservedintronicsequencesbycomparativeanalysisofintronsSearchingconservedintergenicsequencesSearchingwell-definedsequenceelementsorcharacteristics(boxC/D,functionalregions,complementaryandotherconservedsequenceetc.)NovelalgorithmtakingthefoldingparametersinRNAmoleculeintoaccountAllpredictionsofnovelncRNAgenesneedtobeconfirmedbydirectdetectionofthesetranscripts!!!AComputationalScreenforMethylationGuidesnoRNAsSCIENCE,283:1168-1171,FEBRUARY19,1999AexampleofcomputationalapproachforscreeningboxC/DsnoRNAsSimilaritySearchingProteinsBLAST,SequenceAlignmentGenesthatcodeforproteinsareconservedacrossgenomes(e.g.lowrateofmutation)ncRNASecondarystructureusuallyconservedAlignmentscoringbasedonstructureisimperativeorthologous（a1inspeciesI,a1inspeciesII)paralogous（a1anda2inspeciesI）OrthologousandparalogousRepeatSequencerepeatsequenceInvertedrepeat,palindromesequencemirrorrepeat(Invertedrepeat)GAATTCCTTAAGTriplehelixncRNA:SequencevsStructureThespecificityofRNAsearchncRNAisdefinedbyprimaryandsecondarystructureRNAstructureBase-pairingdefinesasecondarystructureRNAisextremelydifficulttocrystallize:RNAisenzymaticallyunstablemolecule(RNAsesareeverywhere!)RNAisconformationallyflexiblemolecule.ThusBioinformaticapproach–RNAstructurepredictionisveryimportant!TertiarystucturesaremuchlesswellunderstoodL-shapedtRNAmoleculemethodsforfindingnovelnon-codingRNAgenesTraditionalmethodsbyPAGEseparationofnon-codingRNAsandsequencingbyimmunoprecipitationofspecificRNPsbynon-codingRNAenrichedcDNAlibrariesandsequencingbymicroarrayanalysisNewnewmethodbynon-codingRNAlibrariesanddeepsequencingExperimentalRNomicsDeepsequencingFunctionalanalysisCombinationofbioinformaticalmethodsandexperimentalmethodsinncRNAfunctionalanalysisstructureandfunctionalanalysisComputationalAnalysisFunctionalPredictionStructuralPredictionFunctionalAnalysisbyExperimentalMethodNomenclatureofnon-codingRNABacterialRNAs---SmallRNA(sRNA)EukaryoticRNA---Non-codingRNA(ncRNA),functionalRNA(fRNA),smallnonmessengerRNAs(snmRNA)Basedonsubcellularlocalization---SmallnucleolarRNAs(snoRNA)Basedonsize---microRNA(miRNA)，smallinterferingRNAs(siRNA),longnon-codingRNA(lnRNA)BoxC/DandboxH/ACAguidesnoRNAsandthecoreassociatedproteinssnoRNAmethylgroupsorpseudouridinegroupsmethylationandpseudouridylationguidedbysnoRNAsRNAprocessingandmodificationBoxC/DsnoRNA(a)(b)BoxC/DsnoRNAsdirectrRNAmethylationBoxH/ACAsnoRNA(a)(b)BoxH/ACAsnoRNAsdirectrRNApseudouridylationBoxC/D-H/ACAsnoRNA(scaRNA)snoRNAtargetsnoRNA--------------------------------------rRNA,U6scaRNA---------------------------------------snRNAimprintedsnoRNA-------------------------mRNAHomologsofsnoRNAsinArchaea-----rRNAandtRNAOrphanguidesnoRNAs-------------------Notarget(1)(2)(3)(4)DiversityofgenomicorganizationofncRNAsTrendsPlantScience,8(1):42-49,2003snoRNAgneneorganizationDiversityofgenomicorganizationofncRNAsmicroRNAgneneorganizationDiversityofgenomicorganizationofncRNAssnoRNAandmicroRNAgeneclusterPolycistronicandintronicpre-snoRNAtranscriptsareprocessedbyeitherasplicingoranon-splicingpathwayProcessionofpolycistronicandintronicpre-snoRNAtranscriptsNon-codingRNAhostgeneProteinCodingGene------MostintronicsnoRNAgenesofvertebratesandyeastarenestedingenesencodingproteinsinvolvedinribosomebiogenesis.Non-codingRNAgene------These‘‘host’’genesharboursnoRNAsinmultipleintronsbuttheirexondoesnotcodeforproteinsSPAC1B3.05snR80snR90SPAC1B3.05Exon2IntronExon1snR90precursorsnR80NucleasesIntronlariatSplicingExonucleasetrimmingsnR90snR80snR90Exon2IntronExon1PolycistronicprecursorTranscriptionmicroRNAThediscoveryofmiRNAs•miRNAwasfirstdiscoveredin1993byVictorAmbrosatHarvard(lin-4)•ThesecondmiRNALet-7wasdiscoveredin2000byFrankSlackasapostdocatHarvard(Ruvkunlab)VictorAmbrosGaryRuvkunThefirstdiscoveredmiRNAlin-4in1993Ruvk