The regulatory network architecture of cardiometabolic diseases

Transcriptome Fact Sheet - National Human Genome ...

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A transcriptome is a collection of all the gene readouts present in a cell. What is a transcriptome? The human genome is made up of DNA ... Skiptomaincontent TranscriptomeFactSheet Atranscriptomeisacollectionofallthegenereadoutspresentinacell. Whatisatranscriptome? ThehumangenomeismadeupofDNA(deoxyribonucleicacid),along,windingmoleculethatcontainstheinstructionsneededtobuildandmaintaincells.Theseinstructionsarespelledoutintheformof"basepairs"offourdifferentchemicals,organizedinto20,000to25,000genes.Fortheinstructionstobecarriedout,DNAmustbe"read"andtranscribed-inotherwords,copied-intoRNA(ribonucleicacid).Thesegenereadoutsarecalledtranscripts,andatranscriptomeisacollectionofallthegenereadoutspresentinacell. TherearevariouskindsofRNA.Themajortype,calledmessengerRNA(mRNA),playsavitalroleinmakingproteins.Inthisprocess:mRNAistranscribedfromgenes;thenthemRNAtranscriptsaredeliveredtoribosomes,themolecularmachineslocatedinthecell'scytoplasm;thentheribosomesread,or"translate,"thesequenceofchemicallettersinthemRNAandassemblebuildingblockscalledaminoacidsintoproteins. DNAcanalsobetranscribedintoothertypesofRNAthatdonotcodeforproteins.Suchtranscriptsmayservetoinfluencecellstructureandtoregulategenes. Whatisatranscriptome? ThehumangenomeismadeupofDNA(deoxyribonucleicacid),along,windingmoleculethatcontainstheinstructionsneededtobuildandmaintaincells.Theseinstructionsarespelledoutintheformof"basepairs"offourdifferentchemicals,organizedinto20,000to25,000genes.Fortheinstructionstobecarriedout,DNAmustbe"read"andtranscribed-inotherwords,copied-intoRNA(ribonucleicacid).Thesegenereadoutsarecalledtranscripts,andatranscriptomeisacollectionofallthegenereadoutspresentinacell. TherearevariouskindsofRNA.Themajortype,calledmessengerRNA(mRNA),playsavitalroleinmakingproteins.Inthisprocess:mRNAistranscribedfromgenes;thenthemRNAtranscriptsaredeliveredtoribosomes,themolecularmachineslocatedinthecell'scytoplasm;thentheribosomesread,or"translate,"thesequenceofchemicallettersinthemRNAandassemblebuildingblockscalledaminoacidsintoproteins. DNAcanalsobetranscribedintoothertypesofRNAthatdonotcodeforproteins.Suchtranscriptsmayservetoinfluencecellstructureandtoregulategenes. Whatcanatranscriptometellus? AnRNAsequencemirrorsthesequenceoftheDNAfromwhichitwastranscribed.Consequently,byanalyzingtheentirecollectionofRNAsequencesinacell(thetranscriptome)researcherscandeterminewhenandwhereeachgeneisturnedonoroffinthecellsandtissuesofanorganism. Dependingonthetechniqueused,itisoftenpossibletocountthenumberoftranscriptstodeterminetheamountofgeneactivity-alsocalledgeneexpression-inacertaincellortissuetype. Inhumansandotherorganisms,nearlyeverycellcontainsthesamegenes,butdifferentcellsshowdifferentpatternsofgeneexpression.Thesedifferencesareresponsibleforthemanydifferentpropertiesandbehaviorsofvariouscellsandtissues,bothinhealthanddisease. Bycollectingandcomparingtranscriptomesofdifferenttypesofcells,researcherscangainadeeperunderstandingofwhatconstitutesaspecificcelltype,howthattypeofcellnormallyfunctions,andhowchangesinthenormallevelofgeneactivitymayreflectorcontributetodisease.Inaddition,transcriptomesmayenableresearcherstogenerateacomprehensive,genome-widepictureofwhatgenesareactiveinwhichcells.   Whatcanatranscriptometellus? AnRNAsequencemirrorsthesequenceoftheDNAfromwhichitwastranscribed.Consequently,byanalyzingtheentirecollectionofRNAsequencesinacell(thetranscriptome)researcherscandeterminewhenandwhereeachgeneisturnedonoroffinthecellsandtissuesofanorganism. Dependingonthetechniqueused,itisoftenpossibletocountthenumberoftranscriptstodeterminetheamountofgeneactivity-alsocalledgeneexpression-inacertaincellortissuetype. Inhumansandotherorganisms,nearlyeverycellcontainsthesamegenes,butdifferentcellsshowdifferentpatternsofgeneexpression.Thesedifferencesareresponsibleforthemanydifferentpropertiesandbehaviorsofvariouscellsandtissues,bothinhealthanddisease. Bycollectingandcomparingtranscriptomesofdifferenttypesofcells,researcherscangainadeeperunderstandingofwhatconstitutesaspecificcelltype,howthattypeofcellnormallyfunctions,andhowchangesinthenormallevelofgeneactivitymayreflectorcontributetodisease.Inaddition,transcriptomesmayenableresearcherstogenerateacomprehensive,genome-widepictureofwhatgenesareactiveinwhichcells.   Howtranscriptomesbeusedtoexploregenefunction? Thefunctionofmostgenesisnotyetknown.Asearchofatranscriptomedatabasecangiveresearchersalistofallthetissuesinwhichageneisexpressed,providingcluesaboutitspossiblefunction. Forexample,ifthetranscriptomedatabaseshowsthatanunknowngene'sexpressionlevelsaredramaticallyhigherincancercellsthaninhealthycells,theunknowngenemayplayaroleincellgrowth.Orifanunknowngeneisexpressedinfattissuebutnotinboneormuscletissue,theunknowngenemaybeinvolvedinfatstorageormetabolism.Inbothinstances,thetranscriptomedatagiveresearchersagoodplacetostartsearchingforanewlyfoundgene'sfunction. TheNationalHumanGenomeResearchInstitute(NHGRI),whichispartoftheNationalInstitutesofHealth(NIH),hasparticipatedintwoprojectsthatcreatedtranscriptomeresourcesforresearchersaroundtheworld-theMammalianGeneCollectioninitiativeandtheMouseTranscriptomeProject. TheMammalianGeneCollectioninitiativebuiltafree,publiclibraryofhuman,mouse,andratmRNAsequences.TheprojectwasledbyNHGRIandtheNationalCancerInstitute(NCI),alsopartofNIH.Themouseandratareimportantmodelswithwhichtostudyhumanbiology. TheMouseTranscriptomeProjectwasanNIH-supportedinitiativethatgeneratedafree,publicdatabaseofgenetranscriptsformanymousetissues.Thesetissue-specificgeneexpressiondata,whicharemappedtothemousegenome,areavailableinasearchableformatintheMouseReferenceTranscriptomeDatabase. Severalothertranscriptomeresourcesexist,includingthoseinNIHprogramssuchastheGenotype-TissueExpressionProject(GTEx)andtheEncyclopediaofDNAElements(ENCODE).GTExiscreatingacatalogofhumangeneexpressioninavarietyofdifferenttissues.ENCODEresearchersaimtocharacterizeandunderstandtheworkingpartsofthegenome,includingthetranscriptome.BothNovartisandtheEuropeanMolecularBiologyLaboratoryhavewell-establishedgeneexpressiondatabases. Howtranscriptomesbeusedtoexploregenefunction? Thefunctionofmostgenesisnotyetknown.Asearchofatranscriptomedatabasecangiveresearchersalistofallthetissuesinwhichageneisexpressed,providingcluesaboutitspossiblefunction. Forexample,ifthetranscriptomedatabaseshowsthatanunknowngene'sexpressionlevelsaredramaticallyhigherincancercellsthaninhealthycells,theunknowngenemayplayaroleincellgrowth.Orifanunknowngeneisexpressedinfattissuebutnotinboneormuscletissue,theunknowngenemaybeinvolvedinfatstorageormetabolism.Inbothinstances,thetranscriptomedatagiveresearchersagoodplacetostartsearchingforanewlyfoundgene'sfunction. TheNationalHumanGenomeResearchInstitute(NHGRI),whichispartoftheNationalInstitutesofHealth(NIH),hasparticipatedintwoprojectsthatcreatedtranscriptomeresourcesforresearchersaroundtheworld-theMammalianGeneCollectioninitiativeandtheMouseTranscriptomeProject. TheMammalianGeneCollectioninitiativebuiltafree,publiclibraryofhuman,mouse,andratmRNAsequences.TheprojectwasledbyNHGRIandtheNationalCancerInstitute(NCI),alsopartofNIH.Themouseandratareimportantmodelswithwhichtostudyhumanbiology. TheMouseTranscriptomeProjectwasanNIH-supportedinitiativethatgeneratedafree,publicdatabaseofgenetranscriptsformanymousetissues.Thesetissue-specificgeneexpressiondata,whicharemappedtothemousegenome,areavailableinasearchableformatintheMouseReferenceTranscriptomeDatabase. Severalothertranscriptomeresourcesexist,includingthoseinNIHprogramssuchastheGenotype-TissueExpressionProject(GTEx)andtheEncyclopediaofDNAElements(ENCODE).GTExiscreatingacatalogofhumangeneexpressioninavarietyofdifferenttissues.ENCODEresearchersaimtocharacterizeandunderstandtheworkingpartsofthegenome,includingthetranscriptome.BothNovartisandtheEuropeanMolecularBiologyLaboratoryhavewell-establishedgeneexpressiondatabases. Lastupdated:August17,2020

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