Transcriptome - Wikipedia

The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes ... Transcriptome FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch SetofallRNAmoleculesinonecellorapopulationofcells ThetranscriptomeisthesetofallRNAtranscripts,includingcodingandnon-coding,inanindividualorapopulationofcells.ThetermcanalsosometimesbeusedtorefertoallRNAs,orjustmRNA,dependingontheparticularexperiment.Thetermtranscriptomeisaportmanteauofthewordstranscriptandgenome;itisassociatedwiththeprocessoftranscriptproductionduringthebiologicalprocessoftranscription. TheearlystagesoftranscriptomeannotationsbeganwithcDNAlibrariespublishedinthe1980s.Subsequently,theadventofhigh-throughputtechnologyledtofasterandmoreefficientwaysofobtainingdataaboutthetranscriptome.Twobiologicaltechniquesareusedtostudythetranscriptome,namelyDNAmicroarray,ahybridization-basedtechniqueandRNA-seq,asequence-basedapproach.[1]RNA-seqisthepreferredmethodandhasbeenthedominanttranscriptomicstechniquesincethe2010s.Single-celltranscriptomicsallowstrackingoftranscriptchangesovertimewithinindividualcells. Dataobtainedfromthetranscriptomeisusedinresearchtogaininsightintoprocessessuchascellulardifferentiation,carcinogenesis,transcriptionregulationandbiomarkerdiscoveryamongothers.Transcriptome-obtaineddataalsofindsapplicationsinestablishingphylogeneticrelationshipsduringtheprocessofevolutionandininvitrofertilization.Thetranscriptomeiscloselyrelatedtoother-omebasedbiologicalfieldsofstudy;itiscomplementarytotheproteomeandthemetabolomeandencompassesthetranslatome,exome,meiomeandthanatotranscriptomewhichcanbeseenasomefieldsstudyingspecifictypesofRNAtranscripts.ThearequantifiableandconservedrelationshipsbetweentheTranscriptomeandother-omes,andTranscriptomicsdatacanbeusedeffectivelytopredictothermolecularspecies,suchasmetabolites.[2]Therearenumerouspubliclyavailabletranscriptomedatabases. Contents 1Etymologyandhistory 2Transcription 3TypesofRNAtranscripts 4Scopeofstudy 5Methodsofconstruction 5.1DNAmicroarrays 5.2RNAsequencing 5.3Single-celltranscriptomics 6Analysis 7Applications 7.1Mammals 7.2Plants 8Relationtootheromefields 8.1Relationtoproteome 9Transcriptomedatabases 10Seealso 11Notes 12References 13Furtherreading Etymologyandhistory[edit] Thewordtranscriptomeisaportmanteauofthewordstranscriptandgenome.Itappearedalongwithotherneologismsformedusingthesuffixes-omeand-omicstodenoteallstudiesconductedonagenome-widescaleinthefieldsoflifesciencesandtechnology.Assuch,transcriptomeandtranscriptomicswereoneofthefirstwordstoemergealongwithgenomeandproteome.[3]ThefirststudytopresentacaseofacollectionofacDNAlibraryforsilkmothmRNAwaspublishedin1979.[4]Thefirstseminalstudytomentionandinvestigatethetranscriptomeofanorganismwaspublishedin1997anditdescribed60,633transcriptsexpressedinS.cerevisiaeusingserialanalysisofgeneexpression(SAGE).[5]Withtheriseofhigh-throughputtechnologiesandbioinformaticsandthesubsequentincreasedcomputationalpower,itbecameincreasinglyefficientandeasytocharacterizeandanalyzeenormousamountofdata.[3]AttemptstocharacterizethetranscriptomebecamemoreprominentwiththeadventofautomatedDNAsequencingduringthe1980s.[6]Duringthe1990s,expressedsequencetagsequencingwasusedtoidentifygenesandtheirfragments.[7]Thiswasfollowedbytechniquessuchasserialanalysisofgeneexpression(SAGE),capanalysisofgeneexpression(CAGE),andmassivelyparallelsignaturesequencing(MPSS). Transcription[edit] Seealso:Transcription(biology) Thetranscriptomeencompassesalltheribonucleicacid(RNA)transcriptspresentinagivenorganismorexperimentalsample.[8]RNAisthemaincarrierofgeneticinformationthatisresponsiblefortheprocessofconvertingDNAintoanorganism'sphenotype.Agenecangiverisetoasingle-strandedmessengerRNA(mRNA)throughamolecularprocessknownastranscription;thismRNAiscomplementarytothestrandofDNAitoriginatedfrom.[6]TheenzymeRNApolymeraseIIattachestothetemplateDNAstrandandcatalyzestheadditionofribonucleotidestothe3'endofthegrowingsequenceofthemRNAtranscript.[9] Inordertoinitiateitsfunction,RNApolymeraseIIneedstorecognizeapromotersequence,locatedupstream(5')ofthegene.Ineukaryotes,thisprocessismediatedbytranscriptionfactors,mostnotablyTranscriptionfactorIID(TFIID)whichrecognizestheTATAboxandaidsinthepositioningofRNApolymeraseattheappropriatestartsite.TofinishtheproductionoftheRNAtranscript,terminationtakesplaceusuallyseveralhundrednuclecotidesawayfromtheterminationsequenceandcleavagetakesplace.[9]ThisprocessoccursinthenucleusofacellalongwithRNAprocessingbywhichmRNAmoleculesarecapped,splicedandpolyadenylatedtoincreasetheirstabilitybeforebeingsubsequentlytakentothecytoplasm.ThemRNAgivesrisetoproteinsthroughtheprocessoftranslationthattakesplaceinribosomes. TypesofRNAtranscripts[edit] Inaccordancewiththecentraldogmaofmolecularbiology,thetranscriptomeinitiallyencompassedonlyprotein-codingmRNAtranscripts.Nevertheless,severalRNAsubtypeswithdistinctfunctionsexist.ManyRNAtranscriptsdonotcodeforproteinorhavedifferentregulatoryfunctionsintheprocessofgenetranscriptionandtranslation.RNAtypeswhichdonotfallwithinthescopeofthecentraldogmaofmolecularbiologyarenon-codingRNAswhichcanbedividedintotwogroupsoflongnon-codingRNAandshortnon-codingRNA. Longnon-codingRNAincludesallnon-codingRNAtranscriptsthataremorethan200nucleotideslong.Membersofthisgroupcomprisethelargestfractionofthenon-codingtranscriptome.Shortnon-codingRNAincludesthefollowingmembers: transferRNA(tRNA) microRNA(miRNA):19-24nucleotides(nt)long.MicroRNAsup-ordownregulateexpressionlevelsofmRNAsbytheprocessofRNAinterferenceatthepost-transcriptionallevel.[3] smallinterferingRNA(siRNA):20-24nt smallnucleolarRNA(snoRNA) Piwi-interactingRNA(piRNA):24-31nt.TheyinteractwithPiwiproteinsoftheArgonautefamilyandhaveafunctionintargetingandcleavingtransposons.[10] enhancerRNA(eRNA)[3] Scopeofstudy[edit] Inthehumangenome,about5%ofallgenesgettranscribedintoRNA.[8]ThetranscriptomeconsistsofcodingmRNAwhichcomprisearound1-4%ofitsentiretyandnon-codingRNAswhichcomprisetherestofthegenomeanddonotgiverisetoproteins.[11][12]Thenumberofnon-protein-codingsequencesincreasesinmorecomplexorganisms.[13] Severalfactorsrenderthecontentofthetranscriptomedifficulttoestablish.Theseincludealternativesplicing,RNAeditingandalternativetranscriptionamongothers.[13]Additionally,transcriptometechniquesarecapableofcapturingtranscriptionoccurringinasampleataspecifictimepoint,althoughthecontentofthetranscriptomecanchangeduringdifferentiation.[6]Themainaimsoftranscriptomicsarethefollowing:"catalogueallspeciesoftranscript,includingmRNAs,non-codingRNAsandsmallRNAs;todeterminethetranscriptionalstructureofgenes,intermsoftheirstartsites,5′and3′ends,splicingpatternsandotherpost-transcriptionalmodifications;andtoquantifythechangingexpressionlevelsofeachtranscriptduringdevelopmentandunderdifferentconditions".[1] Thetermcanbeappliedtothetotalsetoftranscriptsinagivenorganism,ortothespecificsubsetoftranscriptspresentinaparticularcelltype.Unlikethegenome,whichisroughlyfixedforagivencellline(excludingmutations),thetranscriptomecanvarywithexternalenvironmentalconditions.BecauseitincludesallmRNAtranscriptsinthecell,thetranscriptomereflectsthegenesthatarebeingactivelyexpressedatanygiventime,withtheexceptionofmRNAdegradationphenomenasuchastranscriptionalattenuation.Thestudyoftranscriptomics,(whichincludesexpressionprofiling,splicevariantanalysisetc.),examinestheexpressionlevelofRNAsinagivencellpopulation,oftenfocusingonmRNA,butsometimesincludingotherssuchastRNAsandsRNAs. Methodsofconstruction[edit] Mainarticle:Transcriptomicstechnologies Transcriptomicsisthequantitativesciencethatencompassestheassignmentofalistofstrings("reads")totheobject("transcripts"inthegenome).Tocalculatetheexpressionstrength,thedensityofreadscorrespondingtoeachobjectiscounted.[14]Initially,transcriptomeswereanalyzedandstudiedusingexpressedsequencetagslibrariesandserialandcapanalysisofgeneexpression(SAGE). Currently,thetwomaintranscriptomicstechniquesincludeDNAmicroarraysandRNA-Seq.BothtechniquesrequireRNAisolationthroughRNAextractiontechniques,followedbyitsseparationfromothercellularcomponentsandenrichmentofmRNA.[15][16] Therearetwogeneralmethodsofinferringtranscriptomesequences.Oneapproachmapssequencereadsontoareferencegenome,eitheroftheorganismitself(whosetranscriptomeisbeingstudied)orofacloselyrelatedspecies.Theotherapproach,denovotranscriptomeassembly,usessoftwaretoinfertranscriptsdirectlyfromshortsequencereadsandisusedinorganismswithgenomesthatarenotsequenced.[17] DNAmicroarrays[edit] Mainarticle:DNAmicroarray DNAmicroarrayusedtodetectgeneexpressioninhuman(left)andmouse(right)samples Thefirsttranscriptomestudieswerebasedonmicroarraytechniques(alsoknownasDNAchips).Microarraysconsistofthinglasslayerswithspotsonwhicholigonucleotides,knownas"probes"arearrayed;eachspotcontainsaknownDNAsequence.[18] Whenperformingmicroarrayanalyses,mRNAiscollectedfromacontrolandanexperimentalsample,thelatterusuallyrepresentativeofadisease.TheRNAofinterestisconvertedtocDNAtoincreaseitsstabilityandmarkedwithfluorophoresoftwocolors,usuallygreenandred,forthetwogroups.ThecDNAisspreadontothesurfaceofthemicroarraywhereithybridizeswitholigonucleotidesonthechipandalaserisusedtoscan.Thefluorescenceintensityoneachspotofthemicroarraycorrespondstothelevelofgeneexpressionandbasedonthecolorofthefluorophoresselected,itcanbedeterminedwhichofthesamplesexhibitshigherlevelsofthemRNAofinterest.[7] Onemicroarrayusuallycontainsenougholigonucleotidestorepresentallknowngenes;however,dataobtainedusingmicroarraysdoesnotprovideinformationaboutunknowngenes.Duringthe2010s,microarrayswerealmostcompletelyreplacedbynext-generationtechniquesthatarebasedonDNAsequencing. RNAsequencing[edit] Mainarticle:RNA-Seq RNAsequencingisanext-generationsequencingtechnology;assuchitrequiresonlyasmallamountofRNAandnopreviousknowledgeofthegenome.[3]ItallowsforbothqualitativeandquantitativeanalysisofRNAtranscripts,theformerallowingdiscoveryofnewtranscriptsandthelatterameasureofrelativequantitiesfortranscriptsinasample.[10] ThethreemainstepsofsequencingtranscriptomesofanybiologicalsamplesincludeRNApurification,thesynthesisofanRNAorcDNAlibraryandsequencingthelibrary.[10]TheRNApurificationprocessisdifferentforshortandlongRNAs.[10]ThisstepisusuallyfollowedbyanassessmentofRNAquality,withthepurposeofavoidingcontaminantssuchasDNAortechnicalcontaminantsrelatedtosampleprocessing.RNAqualityismeasuredusingUVspectrometrywithanabsorbancepeakof260 nm.[19]RNAintegritycanalsobeanalyzedquantitativelycomparingtheratioandintensityof28SRNAto18SRNAreportedintheRNAIntegrityNumber(RIN)score.[19]SincemRNAisthespeciesofinterestanditrepresentsonly3%ofitstotalcontent,theRNAsampleshouldbetreatedtoremoverRNAandtRNAandtissue-specificRNAtranscripts.[19] ThestepoflibrarypreparationwiththeaimofproducingshortcDNAfragments,beginswithRNAfragmentationtotranscriptsinlengthbetween50and300basepairs.Fragmentationcanbeenzymatic(RNAendonucleases),chemical(trismagnesiumsaltbuffer,chemicalhydrolysis)ormechanical(sonication,nebulisation).[20]ReversetranscriptionisusedtoconverttheRNAtemplatesintocDNAandthreeprimingmethodscanbeusedtoachieveit,includingoligo-DT,usingrandomprimersorligatingspecialadaptoroligos. Single-celltranscriptomics[edit] Mainarticle:Single-celltranscriptomics Transcriptioncanalsobestudiedatthelevelofindividualcellsbysingle-celltranscriptomics.Single-cellRNAsequencing(scRNA-seq)isarecentlydevelopedtechniquethatallowstheanalysisofthetranscriptomeofsinglecells.Withsingle-celltranscriptomics,subpopulationsofcelltypesthatconstitutethetissueofinterestarealsotakenintoconsideration.[21]Thisapproachallowstoidentifywhetherchangesinexperimentalsamplesareduetophenotypiccellularchangesasopposedtoproliferation,withwhichaspecificcelltypemightbeoverexpressedinthesample.[22]Additionally,whenassessingcellularprogressionthroughdifferentiation,averageexpressionprofilesareonlyabletoordercellsbytimeratherthantheirstageofdevelopmentandareconsequentlyunabletoshowtrendsingeneexpressionlevelsspecifictocertainstages.[23]Single-celltrarnscriptomictechniqueshavebeenusedtocharacterizerarecellpopulationssuchascirculatingtumorcells,cancerstemcellsinsolidtumors,andembryonicstemcells(ESCs)inmammalianblastocysts.[24] Althoughtherearenostandardizedtechniquesforsingle-celltranscriptomics,severalstepsneedtobeundertaken.Thefirststepincludescellisolation,whichcanbeperformedusinglow-andhigh-throughputtechniques.ThisisfollowedbyaqPCRstepandthensingle-cellRNAseqwheretheRNAofinterestisconvertedintocDNA.Newerdevelopmentsinsingle-celltranscriptomicsallowfortissueandsub-cellularlocalizationpreservationthroughcryo-sectioningthinslicesoftissuesandsequencingthetranscriptomeineachslice.Anothertechniqueallowsthevisualizationofsingletranscriptsunderamicroscopewhilepreservingthespatialinformationofeachindividualcellwheretheyareexpressed.[24] Analysis[edit] Anumberoforganism-specifictranscriptomedatabaseshavebeenconstructedandannotatedtoaidintheidentificationofgenesthataredifferentiallyexpressedindistinctcellpopulations. RNA-seqisemerging(2013)asthemethodofchoiceformeasuringtranscriptomesoforganisms,thoughtheoldertechniqueofDNAmicroarraysisstillused.[1]RNA-seqmeasuresthetranscriptionofaspecificgenebyconvertinglongRNAsintoalibraryofcDNAfragments.ThecDNAfragmentsarethensequencedusinghigh-throughputsequencingtechnologyandalignedtoareferencegenomeortranscriptomewhichisthenusedtocreateanexpressionprofileofthegenes.[1] Applications[edit] Mammals[edit] Thetranscriptomesofstemcellsandcancercellsareofparticularinteresttoresearcherswhoseektounderstandtheprocessesofcellulardifferentiationandcarcinogenesis.ApipelineusingRNA-seqorgenearraydatacanbeusedtotrackgeneticchangesoccurringinstemandprecursorcellsandrequiresatleastthreeindependentgeneexpressiondatafromtheformercelltypeandmaturecells.[25] Analysisofthetranscriptomesofhumanoocytesandembryosisusedtounderstandthemolecularmechanismsandsignalingpathwayscontrollingearlyembryonicdevelopment,andcouldtheoreticallybeapowerfultoolinmakingproperembryoselectionininvitrofertilisation.[citationneeded]Analysesofthetranscriptomecontentoftheplacentainthefirst-trimesterofpregnancyininvitrofertilizationandembryotransfer(IVT-ET)revealeddifferencesingeneticexpressionwhichareassociatedwithhigherfrequencyofadverseperinataloutcomes.Suchinsightcanbeusedtooptimizethepractice.[26]Transcriptomeanalysescanalsobeusedtooptimizecryopreservationofoocytes,byloweringinjuriesassociatedwiththeprocess.[27] Transcriptomicsisanemergingandcontinuallygrowingfieldinbiomarkerdiscoveryforuseinassessingthesafetyofdrugsorchemicalriskassessment.[28] Transcriptomesmayalsobeusedtoinferphylogeneticrelationshipsamongindividualsortodetectevolutionarypatternsoftranscriptomeconservation.[29] Transcriptomeanalyseswereusedtodiscovertheincidenceofantisensetranscription,theirroleingeneexpressionthroughinteractionwithsurroundinggenesandtheirabundanceindifferentchromosomes.[30]RNA-seqwasalsousedtoshowhowRNAisoforms,transcriptsstemmingfromthesamegenebutwithdifferentstructures,canproducecomplexphenotypesfromlimitedgenomes.[17] Plants[edit] Transcriptomeanalysishavebeenusedtostudytheevolutionanddiversificationprocessofplantspecies.In2014,the1000PlantGenomesProjectwascompletedinwhichthetranscriptomesof1,124plantspeciesfromthefamiliesviridiplantae,glaucophytaandrhodophytaweresequenced.Theproteincodingsequencesweresubsequentlycomparedtoinferphylogeneticrelationshipsbetweenplantsandtocharacterizethetimeoftheirdiversificationintheprocessofevolution.[31]Transcriptomestudieshavebeenusedtocharacterizeandquantifygeneexpressioninmaturepollen.Genesinvolvedincellwallmetabolismandcytoskeletonwerefoundtobeoverexpressed.Transcriptomeapproachesalsoallowedtotrackchangesingeneexpressionthroughdifferentdevelopmentalstagesofpollen,rangingfrommicrosporetomaturepollengrains;additionallysuchstagescouldbecomparedacrossspeciesofdifferentplantsincludingArabidopsis,riceandtobacco.[32] Relationtootheromefields[edit] Generalschemashowingtherelationshipsofthegenome,transcriptome,proteome,andmetabolome(lipidome). Similartoother-omebasedtechnologies,analysisofthetranscriptomeallowsforanunbiasedapproachwhenvalidatinghypothesesexperimentally.Thisapproachalsoallowsforthediscoveryofnovelmediatorsinsignalingpathways.[14]Aswithother-omicsbasedtechnologies,thetranscriptomecanbeanalyzedwithinthescopeofamultiomicsapproach.Itiscomplementarytometabolomicsbutcontrarytoproteomics,adirectassociationbetweenatranscriptandmetabolitecannotbeestablished. Thereareseveral-omefieldsthatcanbeseenassubcategoriesofthetranscriptome.TheexomediffersfromthetranscriptomeinthatitincludesonlythoseRNAmoleculesfoundinaspecifiedcellpopulation,andusuallyincludestheamountorconcentrationofeachRNAmoleculeinadditiontothemolecularidentities.Additionally,thetranscritpomealsodiffersfromthetranslatome,whichisthesetofRNAsundergoingtranslation. ThetermmeiomeisusedinfunctionalgenomicstodescribethemeiotictranscriptomeorthesetofRNAtranscriptsproducedduringtheprocessofmeiosis.[33]Meiosisisakeyfeatureofsexuallyreproducingeukaryotes,andinvolvesthepairingofhomologouschromosome,synapseandrecombination.Sincemeiosisinmostorganismsoccursinashorttimeperiod,meiotictranscriptprofilingisdifficultduetothechallengeofisolation(orenrichment)ofmeioticcells(meiocytes).Aswithtranscriptomeanalyses,themeiomecanbestudiedatawhole-genomelevelusinglarge-scaletranscriptomictechniques.[34]Themeiomehasbeenwell-characterizedinmammalandyeastsystemsandsomewhatlessextensivelycharacterizedinplants.[35] ThethanatotranscriptomeconsistsofallRNAtranscriptsthatcontinuetobeexpressedorthatstartgettingre-expressedininternalorgansofadeadbody24–48hoursfollowingdeath.Somegenesincludethosethatareinhibitedafterfetaldevelopment.Ifthethanatotranscriptomeisrelatedtotheprocessofprogrammedcelldeath(apoptosis),itcanbereferredtoastheapoptoticthanatotranscriptome.Analysesofthethanatotranscriptomeareusedinforensicmedicine.[36] eQTLmappingcanbeusedtocomplementgenomicswithtranscriptomics;geneticvariantsatDNAlevelandgeneexpressionmeasuresatRNAlevel.[37] Relationtoproteome[edit] Furtherinformation:Proteome Thetranscriptomecanbeseenasasubsetoftheproteome,thatis,theentiresetofproteinsexpressedbyagenome. However,theanalysisofrelativemRNAexpressionlevelscanbecomplicatedbythefactthatrelativelysmallchangesinmRNAexpressioncanproducelargechangesinthetotalamountofthecorrespondingproteinpresentinthecell.Oneanalysismethod,knownasgenesetenrichmentanalysis,identifiescoregulatedgenenetworksratherthanindividualgenesthatareup-ordown-regulatedindifferentcellpopulations.[1] AlthoughmicroarraystudiescanrevealtherelativeamountsofdifferentmRNAsinthecell,levelsofmRNAarenotdirectlyproportionaltotheexpressionleveloftheproteinstheycodefor.[38]ThenumberofproteinmoleculessynthesizedusingagivenmRNAmoleculeasatemplateishighlydependentontranslation-initiationfeaturesofthemRNAsequence;inparticular,theabilityofthetranslationinitiationsequenceisakeydeterminantintherecruitingofribosomesforproteintranslation. 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