Gene expression - Wikipedia

Regulation of gene expressionEdit · A constitutive gene is a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed ... Geneexpression FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Conversionofagene'ssequenceintoamaturegeneproductorproducts Forvocabulary,seeGlossaryofgeneexpressionterms.Foranon-technicalintroductiontothetopic,seeIntroductiontogenetics. Theextendedcentraldogmaofmolecularbiologyincludesallthecellularprocessesinvolvedintheflowofgeneticinformation PartofaseriesonBiochemistryChemistryoflife Index Outline History Keycomponents Biomolecules Enzymes Geneexpression Metabolism Listofbiochemists Biochemist Listofbiochemists Glossaries Glossaryofbiology Glossaryofchemistry  Categoryvte Geneexpressionistheprocessbywhichinformationfromageneisusedinthesynthesisofafunctionalgeneproductthatenablesittoproduceendproducts,proteinornon-codingRNA,andultimatelyaffectaphenotype,asthefinaleffect.Theseproductsareoftenproteins,butinnon-protein-codinggenessuchastransferRNA(tRNA)andsmallnuclearRNA(snRNA),theproductisafunctionalnon-codingRNA.GeneexpressionissummarizedinthecentraldogmaofmolecularbiologyfirstformulatedbyFrancisCrickin1958,[1]furtherdevelopedinhis1970article,[2]andexpandedbythesubsequentdiscoveriesofreversetranscription[3][4][5]andRNAreplication.[6] Theprocessofgeneexpressionisusedbyallknownlife—eukaryotes(includingmulticellularorganisms),prokaryotes(bacteriaandarchaea),andutilizedbyviruses—togeneratethemacromolecularmachineryforlife. Ingenetics,geneexpressionisthemostfundamentallevelatwhichthegenotypegivesrisetothephenotype,i.e.observabletrait.ThegeneticinformationstoredinDNArepresentsthegenotype,whereasthephenotyperesultsfromthe"interpretation"ofthatinformation.Suchphenotypesareoftendisplayedbythesynthesisofproteinsthatcontroltheorganism'sstructureanddevelopment,orthatactasenzymescatalyzingspecificmetabolicpathways. Allstepsinthegeneexpressionprocessmaybemodulated(regulated),includingthetranscription,RNAsplicing,translation,andpost-translationalmodificationofaprotein.Regulationofgeneexpressiongivescontroloverthetiming,location,andamountofagivengeneproduct(proteinorncRNA)presentinacellandcanhaveaprofoundeffectonthecellularstructureandfunction.Regulationofgeneexpressionisthebasisforcellulardifferentiation,development,morphogenesisandtheversatilityandadaptabilityofanyorganism.Generegulationmaythereforeserveasasubstrateforevolutionarychange. Contents 1Mechanism 1.1Transcription 1.2mRNAprocessing 1.3Non-codingRNAmaturation 1.4RNAexport 1.5Translation 1.6Folding 1.7Translocation 1.8Proteintransport 2Regulationofgeneexpression 2.1Transcriptionalregulation 2.1.1Enhancers,transcriptionfactors,mediatorcomplexandDNAloopsinmammaliantranscription 2.2DNAmethylationanddemethylationintranscriptionalregulation 2.3Transcriptionalregulationinlearningandmemory 2.4Transcriptionalregulationincancer 2.5Post-transcriptionalregulation 2.6ThreeprimeuntranslatedregionsandmicroRNAs 2.7Translationalregulation 2.8Post-translationalmodifications 3Measurement 3.1mRNAquantification 3.2RNAprofilesinWikipedia 3.3Proteinquantification 3.4mRNA-proteincorrelation 3.5Localisation 4Expressionsystem 4.1Inducibleexpression 4.2Innature 5Genenetworks 6Techniquesandtools 7Geneexpressiondatabases 8Seealso 9References 10Externallinks Mechanism[edit] Transcription[edit] TheprocessoftranscriptioniscarriedoutbyRNApolymerase(RNAP),whichusesDNA(black)asatemplateandproducesRNA(blue). Mainarticle:Transcription(biology) TheproductionofaRNAcopyfromaDNAstrandiscalledtranscription,andisperformedbyRNApolymerases,whichaddoneribonucleotideatatimetoagrowingRNAstrandasperthecomplementaritylawofthenucleotidebases.ThisRNAiscomplementarytothetemplate3′→5′DNAstrand,[7]withtheexceptionthatthymines(T)arereplacedwithuracils(U)intheRNA. Inprokaryotes,transcriptioniscarriedoutbyasingletypeofRNApolymerase,whichneedstobindaDNAsequencecalledaPribnowboxwiththehelpofthesigmafactorprotein(σfactor)tostarttranscription.Ineukaryotes,transcriptionisperformedinthenucleusbythreetypesofRNApolymerases,eachofwhichneedsaspecialDNAsequencecalledthepromoterandasetofDNA-bindingproteins—transcriptionfactors—toinitiatetheprocess(seeregulationoftranscriptionbelow).RNApolymeraseIisresponsiblefortranscriptionofribosomalRNA(rRNA)genes.RNApolymeraseII(PolII)transcribesallprotein-codinggenesbutalsosomenon-codingRNAs(e.g.,snRNAs,snoRNAsorlongnon-codingRNAs).RNApolymeraseIIItranscribes5SrRNA,transferRNA(tRNA)genes,andsomesmallnon-codingRNAs(e.g.,7SK).Transcriptionendswhenthepolymeraseencountersasequencecalledtheterminator. mRNAprocessing[edit] Mainarticle:Post-transcriptionalmodification Whiletranscriptionofprokaryoticprotein-codinggenescreatesmessengerRNA(mRNA)thatisreadyfortranslationintoprotein,transcriptionofeukaryoticgenesleavesaprimarytranscriptofRNA(pre-RNA),whichfirsthastoundergoaseriesofmodificationstobecomeamatureRNA.Typesandstepsinvolvedinthematurationprocessesvarybetweencodingandnon-codingpreRNAs;i.e.eventhoughpreRNAmoleculesforbothmRNAandtRNAundergosplicing,thestepsandmachineryinvolvedaredifferent.[8]Theprocessingofnon-codingRNAisdescribedbelow(non-coringRNAmaturation). TheprocessingofpremRNAinclude5′capping,whichissetofenzymaticreactionsthatadd7-methylguanosine(m7G)tothe5′endofpre-mRNAandthusprotecttheRNAfromdegradationbyexonucleases.Them7Gcapisthenboundbycapbindingcomplexheterodimer(CBC20/CBC80),whichaidsinmRNAexporttocytoplasmandalsoprotecttheRNAfromdecapping. Anothermodificationis3′cleavageandpolyadenylation.Theyoccurifpolyadenylationsignalsequence(5′-AAUAAA-3′)ispresentinpre-mRNA,whichisusuallybetweenprotein-codingsequenceandterminator.Thepre-mRNAisfirstcleavedandthenaseriesof~200adenines(A)areaddedtoformpoly(A)tail,whichprotectstheRNAfromdegradation.Thepoly(A)tailisboundbymultiplepoly(A)-bindingproteins(PABPs)necessaryformRNAexportandtranslationre-initiation.Intheinverseprocessofdeadenylation,poly(A)tailsareshortenedbytheCCR4-Not3′-5′exonuclease,whichoftenleadstofulltranscriptdecay. Illustrationofexonsandintronsinpre-mRNAandtheformationofmaturemRNAbysplicing.TheUTRs(ingreen)arenon-codingpartsofexonsattheendsofthemRNA. Averyimportantmodificationofeukaryoticpre-mRNAisRNAsplicing.Themajorityofeukaryoticpre-mRNAsconsistofalternatingsegmentscalledexonsandintrons.Duringtheprocessofsplicing,anRNA-proteincatalyticalcomplexknownasspliceosomecatalyzestwotransesterificationreactions,whichremoveanintronandreleaseitinformoflariatstructure,andthenspliceneighbouringexonstogether.Incertaincases,someintronsorexonscanbeeitherremovedorretainedinmaturemRNA.Thisso-calledalternativesplicingcreatesseriesofdifferenttranscriptsoriginatingfromasinglegene.Becausethesetranscriptscanbepotentiallytranslatedintodifferentproteins,splicingextendsthecomplexityofeukaryoticgeneexpressionandthesizeofaspeciesproteome. ExtensiveRNAprocessingmaybeanevolutionaryadvantagemadepossiblebythenucleusofeukaryotes.Inprokaryotes,transcriptionandtranslationhappentogether,whilstineukaryotes,thenuclearmembraneseparatesthetwoprocesses,givingtimeforRNAprocessingtooccur. Non-codingRNAmaturation[edit] Mainarticles:tRNAmaturation,rRNAmaturation,andmiRNAmaturation Inmostorganismsnon-codinggenes(ncRNA)aretranscribedasprecursorsthatundergofurtherprocessing.InthecaseofribosomalRNAs(rRNA),theyareoftentranscribedasapre-rRNAthatcontainsoneormorerRNAs.Thepre-rRNAiscleavedandmodified(2′-O-methylationandpseudouridineformation)atspecificsitesbyapproximately150differentsmallnucleolus-restrictedRNAspecies,calledsnoRNAs.SnoRNAsassociatewithproteins,formingsnoRNPs.WhilesnoRNApartbasepairwiththetargetRNAandthuspositionthemodificationataprecisesite,theproteinpartperformsthecatalyticalreaction.Ineukaryotes,inparticularasnoRNPcalledRNase,MRPcleavesthe45Spre-rRNAintothe28S,5.8S,and18SrRNAs.TherRNAandRNAprocessingfactorsformlargeaggregatescalledthenucleolus.[9] InthecaseoftransferRNA(tRNA),forexample,the5′sequenceisremovedbyRNaseP,[10]whereasthe3′endisremovedbythetRNaseZenzyme[11]andthenon-templated3′CCAtailisaddedbyanucleotidyltransferase.[12]InthecaseofmicroRNA(miRNA),miRNAsarefirsttranscribedasprimarytranscriptsorpri-miRNAwithacapandpoly-Atailandprocessedtoshort,70-nucleotidestem-loopstructuresknownaspre-miRNAinthecellnucleusbytheenzymesDroshaandPasha.Afterbeingexported,itisthenprocessedtomaturemiRNAsinthecytoplasmbyinteractionwiththeendonucleaseDicer,whichalsoinitiatestheformationoftheRNA-inducedsilencingcomplex(RISC),composedoftheArgonauteprotein. EvensnRNAsandsnoRNAsthemselvesundergoseriesofmodificationbeforetheybecomepartoffunctionalRNPcomplex.ThisisdoneeitherinthenucleoplasmorinthespecializedcompartmentscalledCajalbodies.TheirbasesaremethylatedorpseudouridinilatedbyagroupofsmallCajalbody-specificRNAs(scaRNAs),whicharestructurallysimilartosnoRNAs. RNAexport[edit] Mainarticle:Nucleartransport IneukaryotesmostmatureRNAmustbeexportedtothecytoplasmfromthenucleus.WhilesomeRNAsfunctioninthenucleus,manyRNAsaretransportedthroughthenuclearporesandintothecytosol.[13]ExportofRNAsrequiresassociationwithspecificproteinsknownasexportins.SpecificexportinmoleculesareresponsiblefortheexportofagivenRNAtype.mRNAtransportalsorequiresthecorrectassociationwithExonJunctionComplex(EJC),whichensuresthatcorrectprocessingofthemRNAiscompletedbeforeexport.InsomecasesRNAsareadditionallytransportedtoaspecificpartofthecytoplasm,suchasasynapse;theyarethentowedbymotorproteinsthatbindthroughlinkerproteinstospecificsequences(called"zipcodes")ontheRNA.[14] Translation[edit] Mainarticle:Translation(genetics) ForsomeRNA(non-codingRNA)thematureRNAisthefinalgeneproduct.[15]InthecaseofmessengerRNA(mRNA)theRNAisaninformationcarriercodingforthesynthesisofoneormoreproteins.mRNAcarryingasingleproteinsequence(commonineukaryotes)ismonocistronicwhilstmRNAcarryingmultipleproteinsequences(commoninprokaryotes)isknownaspolycistronic. Duringthetranslation,tRNAchargedwithaminoacidenterstheribosomeandalignswiththecorrectmRNAtriplet.Ribosomethenaddsaminoacidtogrowingproteinchain. EverymRNAconsistsofthreeparts:a5′untranslatedregion(5′UTR),aprotein-codingregionoropenreadingframe(ORF),anda3′untranslatedregion(3′UTR).Thecodingregioncarriesinformationforproteinsynthesisencodedbythegeneticcodetoformtriplets.EachtripletofnucleotidesofthecodingregioniscalledacodonandcorrespondstoabindingsitecomplementarytoananticodontripletintransferRNA.TransferRNAswiththesameanticodonsequencealwayscarryanidenticaltypeofaminoacid.Aminoacidsarethenchainedtogetherbytheribosomeaccordingtotheorderoftripletsinthecodingregion.TheribosomehelpstransferRNAtobindtomessengerRNAandtakestheaminoacidfromeachtransferRNAandmakesastructure-lessproteinoutofit.[16][17]EachmRNAmoleculeistranslatedintomanyproteinmolecules,onaverage~2800inmammals.[18][19] Inprokaryotestranslationgenerallyoccursatthepointoftranscription(co-transcriptionally),oftenusingamessengerRNAthatisstillintheprocessofbeingcreated.Ineukaryotestranslationcanoccurinavarietyofregionsofthecelldependingonwheretheproteinbeingwrittenissupposedtobe.Majorlocationsarethecytoplasmforsolublecytoplasmicproteinsandthemembraneoftheendoplasmicreticulumforproteinsthatareforexportfromthecellorinsertionintoacellmembrane.Proteinsthataresupposedtobeproducedattheendoplasmicreticulumarerecognisedpart-waythroughthetranslationprocess.Thisisgovernedbythesignalrecognitionparticle—aproteinthatbindstotheribosomeanddirectsittotheendoplasmicreticulumwhenitfindsasignalpeptideonthegrowing(nascent)aminoacidchain.[20] Folding[edit] Mainarticle:Proteinfolding Proteinbefore(left)andafter(right)folding EachproteinexistsasanunfoldedpolypeptideorrandomcoilwhentranslatedfromasequenceofmRNAintoalinearchainofaminoacids.Thispolypeptidelacksanydevelopedthree-dimensionalstructure(thelefthandsideoftheneighboringfigure).Thepolypeptidethenfoldsintoitscharacteristicandfunctionalthree-dimensionalstructurefromarandomcoil.[21]Aminoacidsinteractwitheachothertoproduceawell-definedthree-dimensionalstructure,thefoldedprotein(therighthandsideofthefigure)knownasthenativestate.Theresultingthree-dimensionalstructureisdeterminedbytheaminoacidsequence(Anfinsen'sdogma).[22] Thecorrectthree-dimensionalstructureisessentialtofunction,althoughsomepartsoffunctionalproteinsmayremainunfolded.[23]Failuretofoldintotheintendedshapeusuallyproducesinactiveproteinswithdifferentpropertiesincludingtoxicprions.Severalneurodegenerativeandotherdiseasesarebelievedtoresultfromtheaccumulationofmisfoldedproteins.[24]Manyallergiesarecausedbythefoldingoftheproteins,fortheimmunesystemdoesnotproduceantibodiesforcertainproteinstructures.[25] Enzymescalledchaperonesassistthenewlyformedproteintoattain(foldinto)the3-dimensionalstructureitneedstofunction.[26]Similarly,RNAchaperoneshelpRNAsattaintheirfunctionalshapes.[27]Assistingproteinfoldingisoneofthemainrolesoftheendoplasmicreticulumineukaryotes. Translocation[edit] Secretoryproteinsofeukaryotesorprokaryotesmustbetranslocatedtoenterthesecretorypathway.NewlysynthesizedproteinsaredirectedtotheeukaryoticSec61orprokaryoticSecYEGtranslocationchannelbysignalpeptides.Theefficiencyofproteinsecretionineukaryotesisverydependentonthesignalpeptidewhichhasbeenused.[28] Proteintransport[edit] Manyproteinsaredestinedforotherpartsofthecellthanthecytosolandawiderangeofsignallingsequencesor(signalpeptides)areusedtodirectproteinstowheretheyaresupposedtobe.Inprokaryotesthisisnormallyasimpleprocessduetolimitedcompartmentalisationofthecell.However,ineukaryotesthereisagreatvarietyofdifferenttargetingprocessestoensuretheproteinarrivesatthecorrectorganelle. Notallproteinsremainwithinthecellandmanyareexported,forexample,digestiveenzymes,hormonesandextracellularmatrixproteins.Ineukaryotestheexportpathwayiswelldevelopedandthemainmechanismfortheexportoftheseproteinsistranslocationtotheendoplasmicreticulum,followedbytransportviatheGolgiapparatus.[29][30] Regulationofgeneexpression[edit] Mainarticle:Regulationofgeneexpression Thepatchycoloursofatortoiseshellcataretheresultofdifferentlevelsofexpressionofpigmentationgenesindifferentareasoftheskin. Regulationofgeneexpressionisthecontroloftheamountandtimingofappearanceofthefunctionalproductofagene.Controlofexpressionisvitaltoallowacelltoproducethegeneproductsitneedswhenitneedsthem;inturn,thisgivescellstheflexibilitytoadapttoavariableenvironment,externalsignals,damagetothecell,andotherstimuli.Moregenerally,generegulationgivesthecellcontroloverallstructureandfunction,andisthebasisforcellulardifferentiation,morphogenesisandtheversatilityandadaptabilityofanyorganism. Numeroustermsareusedtodescribetypesofgenesdependingonhowtheyareregulated;theseinclude: Aconstitutivegeneisagenethatistranscribedcontinuallyasopposedtoafacultativegene,whichisonlytranscribedwhenneeded. Ahousekeepinggeneisagenethatisrequiredtomaintainbasiccellularfunctionandsoistypicallyexpressedinallcelltypesofanorganism.Examplesincludeactin,GAPDHandubiquitin.Somehousekeepinggenesaretranscribedatarelativelyconstantrateandthesegenescanbeusedasareferencepointinexperimentstomeasuretheexpressionratesofothergenes. Afacultativegeneisageneonlytranscribedwhenneededasopposedtoaconstitutivegene. Aninduciblegeneisagenewhoseexpressioniseitherresponsivetoenvironmentalchangeordependentonthepositioninthecellcycle. Anystepofgeneexpressionmaybemodulated,fromtheDNA-RNAtranscriptionsteptopost-translationalmodificationofaprotein.Thestabilityofthefinalgeneproduct,whetheritisRNAorprotein,alsocontributestotheexpressionlevelofthegene—anunstableproductresultsinalowexpressionlevel.Ingeneralgeneexpressionisregulatedthroughchanges[31]inthenumberandtypeofinteractionsbetweenmolecules[32]thatcollectivelyinfluencetranscriptionofDNA[33]andtranslationofRNA.[34] Somesimpleexamplesofwheregeneexpressionisimportantare: Controlofinsulinexpressionsoitgivesasignalforbloodglucoseregulation. Xchromosomeinactivationinfemalemammalstopreventan"overdose"ofthegenesitcontains. Cyclinexpressionlevelscontrolprogressionthroughtheeukaryoticcellcycle. Transcriptionalregulation[edit] Mainarticle:Transcriptionalregulation Whenlactoseispresentinaprokaryote,itactsasaninducerandinactivatestherepressorsothatthegenesforlactosemetabolismcanbetranscribed. Regulationoftranscriptioncanbebrokendownintothreemainroutesofinfluence;genetic(directinteractionofacontrolfactorwiththegene),modulationinteractionofacontrolfactorwiththetranscriptionmachineryandepigenetic(non-sequencechangesinDNAstructurethatinfluencetranscription). Thelambdarepressortranscriptionfactor(green)bindsasadimertomajorgrooveofDNAtarget(redandblue)anddisablesinitiationoftranscription.FromPDB:1LMB​. DirectinteractionwithDNAisthesimplestandthemostdirectmethodbywhichaproteinchangestranscriptionlevels.Genesoftenhaveseveralproteinbindingsitesaroundthecodingregionwiththespecificfunctionofregulatingtranscription.TherearemanyclassesofregulatoryDNAbindingsitesknownasenhancers,insulatorsandsilencers.Themechanismsforregulatingtranscriptionarevaried,fromblockingkeybindingsitesontheDNAforRNApolymerasetoactingasanactivatorandpromotingtranscriptionbyassistingRNApolymerasebinding. Theactivityoftranscriptionfactorsisfurthermodulatedbyintracellularsignalscausingproteinpost-translationalmodificationincludingphosphorylation,acetylation,orglycosylation.Thesechangesinfluenceatranscriptionfactor'sabilitytobind,directlyorindirectly,topromoterDNA,torecruitRNApolymerase,ortofavorelongationofanewlysynthesizedRNAmolecule. Thenuclearmembraneineukaryotesallowsfurtherregulationoftranscriptionfactorsbythedurationoftheirpresenceinthenucleus,whichisregulatedbyreversiblechangesintheirstructureandbybindingofotherproteins.[35]Environmentalstimuliorendocrinesignals[36]maycausemodificationofregulatoryproteins[37]elicitingcascadesofintracellularsignals,[38]whichresultinregulationofgeneexpression. Morerecentlyithasbecomeapparentthatthereisasignificantinfluenceofnon-DNA-sequencespecificeffectsontranscription.TheseeffectsarereferredtoasepigeneticandinvolvethehigherorderstructureofDNA,non-sequencespecificDNAbindingproteinsandchemicalmodificationofDNA.IngeneralepigeneticeffectsaltertheaccessibilityofDNAtoproteinsandsomodulatetranscription. Ineukaryotes,DNAisorganizedinformofnucleosomes.NotehowtheDNA(blueandgreen)istightlywrappedaroundtheproteincoremadeofhistoneoctamer(ribboncoils),restrictingaccesstotheDNA.FromPDB:1KX5​. Ineukaryotesthestructureofchromatin,controlledbythehistonecode,regulatesaccesstoDNAwithsignificantimpactsontheexpressionofgenesineuchromatinandheterochromatinareas. Enhancers,transcriptionfactors,mediatorcomplexandDNAloopsinmammaliantranscription[edit] Regulationoftranscriptioninmammals.Anactiveenhancerregulatoryregionisenabledtointeractwiththepromoterregionofitstargetgenebyformationofachromosomeloop.ThiscaninitiatemessengerRNA(mRNA)synthesisbyRNApolymeraseII(RNAPII)boundtothepromoteratthetranscriptionstartsiteofthegene.Theloopisstabilizedbyonearchitecturalproteinanchoredtotheenhancerandoneanchoredtothepromoterandtheseproteinsarejoinedtoformadimer(redzigzags).SpecificregulatorytranscriptionfactorsbindtoDNAsequencemotifsontheenhancer.Generaltranscriptionfactorsbindtothepromoter.Whenatranscriptionfactorisactivatedbyasignal(hereindicatedasphosphorylationshownbyasmallredstaronatranscriptionfactorontheenhancer)theenhancerisactivatedandcannowactivateitstargetpromoter.TheactiveenhanceristranscribedoneachstrandofDNAinoppositedirectionsbyboundRNAPIIs.Mediator(acomplexconsistingofabout26proteinsinaninteractingstructure)communicatesregulatorysignalsfromtheenhancerDNA-boundtranscriptionfactorstothepromoter. Geneexpressioninmammalsisregulatedbymanycis-regulatoryelements,includingcorepromotersandpromoter-proximalelementsthatarelocatednearthetranscriptionstartsitesofgenes,upstreamontheDNA(towardsthe5'regionofthesensestrand).Otherimportantcis-regulatorymodulesarelocalizedinDNAregionsthataredistantfromthetranscriptionstartsites.Theseincludeenhancers,silencers,insulatorsandtetheringelements.[39]Enhancersandtheirassociatedtranscriptionfactorshavealeadingroleintheregulationofgeneexpression.[40] Enhancersaregenomeregionsthatregulategenes.Enhancerscontrolcell-type-specificgeneexpressionprograms,mostoftenbyloopingthroughlongdistancestocomeinphysicalproximitywiththepromotersoftheirtargetgenes.[41]Multipleenhancers,eachoftentensorhundredofthousandsofnucleotidesdistantfromtheirtargetgenes,looptotheirtargetgenepromotersandcoordinatewitheachothertocontrolgeneexpression.[41] Theillustrationshowsanenhancerloopingaroundtocomeintoproximitywiththepromoterofatargetgene.Theloopisstabilizedbyadimerofaconnectorprotein(e.g.dimerofCTCForYY1).Onememberofthedimerisanchoredtoitsbindingmotifontheenhancerandtheothermemberisanchoredtoitsbindingmotifonthepromoter(representedbytheredzigzagsintheillustration).[42]Severalcellfunction-specifictranscriptionfactors(amongtheabout1,600transcriptionfactorsinahumancell)[43]generallybindtospecificmotifsonanenhancer.[44]Asmallcombinationoftheseenhancer-boundtranscriptionfactors,whenbroughtclosetoapromoterbyaDNAloop,governtranscriptionlevelofthetargetgene.Mediator(acomplexusuallyconsistingofabout26proteinsinaninteractingstructure)communicatesregulatorysignalsfromenhancerDNA-boundtranscriptionfactorsdirectlytotheRNApolymeraseII(polII)enzymeboundtothepromoter.[45] Enhancers,whenactive,aregenerallytranscribedfrombothstrandsofDNAwithRNApolymerasesactingintwodifferentdirections,producingtwoeRNAsasillustratedinthefigure.[46]Aninactiveenhancermaybeboundbyaninactivetranscriptionfactor.Phosphorylationofthetranscriptionfactormayactivateitandthatactivatedtranscriptionfactormaythenactivatetheenhancertowhichitisbound(seesmallredstarrepresentingphosphorylationoftranscriptionfactorboundtoenhancerintheillustration).[47]AnactivatedenhancerbeginstranscriptionofitsRNAbeforeactivatingtranscriptionofmessengerRNAfromitstargetgene.[48] DNAmethylationanddemethylationintranscriptionalregulation[edit] DNAmethylationistheadditionofamethylgrouptotheDNAthathappensatcytosine.Theimageshowsacytosinesingleringbaseandamethylgroupaddedontothe5carbon.Inmammals,DNAmethylationoccursalmostexclusivelyatacytosinethatisfollowedbyaguanine. DNAmethylationisawidespreadmechanismforepigeneticinfluenceongeneexpressionandisseeninbacteriaandeukaryotesandhasrolesinheritabletranscriptionsilencingandtranscriptionregulation.Methylationmostoftenoccursonacytosine(seeFigure).Methylationofcytosineprimarilyoccursindinucleotidesequenceswhereacytosineisfollowedbyaguanine,aCpGsite.ThenumberofCpGsitesinthehumangenomeisabout28million.[49]Dependingonthetypeofcell,about70%oftheCpGsiteshaveamethylatedcytosine.[50] MethylationofcytosineinDNAhasamajorroleinregulatinggeneexpression.MethylationofCpGsinapromoterregionofageneusuallyrepressesgenetranscription[51]whilemethylationofCpGsinthebodyofageneincreasesexpression.[52]TETenzymesplayacentralroleindemethylationofmethylatedcytosines.DemethylationofCpGsinagenepromoterbyTETenzymeactivityincreasestranscriptionofthegene.[53] Transcriptionalregulationinlearningandmemory[edit] Mainarticle:Epigeneticsinlearningandmemory Theidentifiedareasofthehumanbrainareinvolvedinmemoryformation. Inarat,contextualfearconditioning(CFC)isapainfullearningexperience.JustoneepisodeofCFCcanresultinalife-longfearfulmemory.[54]AfteranepisodeofCFC,cytosinemethylationisalteredinthepromoterregionsofabout9.17%ofallgenesinthehippocampusneuronDNAofarat.[55]Thehippocampusiswherenewmemoriesareinitiallystored.AfterCFCabout500geneshaveincreasedtranscription(oftenduetodemethylationofCpGsitesinapromoterregion)andabout1,000geneshavedecreasedtranscription(oftenduetonewlyformed5-methylcytosineatCpGsitesinapromoterregion).Thepatternofinducedandrepressedgeneswithinneuronsappearstoprovideamolecularbasisforformingthefirsttransientmemoryofthistrainingeventinthehippocampusoftheratbrain.[55] SomespecificmechanismsguidingnewDNAmethylationsandnewDNAdemethylationsinthehippocampusduringmemoryestablishmenthaverecentlybeenestablished(see[56]forsummary).OnemechanismincludesguidingtheshortisoformoftheTET1DNAdemethylationenzyme,TET1s,toabout600locationsonthegenome.TheguidanceisperformedbyassociationofTET1swithEGR1protein,atranscriptionfactorimportantinmemoryformation.BringingTET1stotheselocationsinitiatesDNAdemethylationatthosesites,up-regulatingassociatedgenes.AsecondmechanisminvolvesDNMT3A2,asplice-isoformofDNAmethyltransferaseDNMT3A,whichaddsmethylgroupstocytosinesinDNA.Thisisoformisinducedbysynapticactivity,anditslocationofactionappearstobedeterminedbyhistonepost-translationalmodifications(ahistonecode).TheresultingnewmessengerRNAsarethentransportedbymessengerRNPparticles(neuronalgranules)tosynapsesoftheneurons,wheretheycanbetranslatedintoproteinsaffectingtheactivitiesofsynapses.[56] Inparticular,thebrain-derivedneurotrophicfactorgene(BDNF)isknownasa"learninggene."[57]AfterCFCtherewasupregulationofBDNFgeneexpression,relatedtodecreasedCpGmethylationofcertaininternalpromotersofthegene,andthiswascorrelatedwithlearning.[57] Transcriptionalregulationincancer[edit] Mainarticle:Regulationoftranscriptionincancer ThemajorityofgenepromoterscontainaCpGislandwithnumerousCpGsites.[58]Whenmanyofagene'spromoterCpGsitesaremethylatedthegenebecomessilenced.[59]Colorectalcancerstypicallyhave3to6drivermutationsand33to66hitchhikerorpassengermutations.[60]However,transcriptionalsilencingmaybeofmoreimportancethanmutationincausingprogressiontocancer.Forexample,incolorectalcancersabout600to800genesaretranscriptionallysilencedbyCpGislandmethylation(seeregulationoftranscriptionincancer).Transcriptionalrepressionincancercanalsooccurbyotherepigeneticmechanisms,suchasalteredexpressionofmicroRNAs.[61]Inbreastcancer,transcriptionalrepressionofBRCA1mayoccurmorefrequentlybyover-transcribedmicroRNA-182thanbyhypermethylationoftheBRCA1promoter(seeLowexpressionofBRCA1inbreastandovariancancers). Post-transcriptionalregulation[edit] Mainarticle:Post-transcriptionalregulation Ineukaryotes,whereexportofRNAisrequiredbeforetranslationispossible,nuclearexportisthoughttoprovideadditionalcontrolovergeneexpression.Alltransportinandoutofthenucleusisviathenuclearporeandtransportiscontrolledbyawiderangeofimportinandexportinproteins. ExpressionofagenecodingforaproteinisonlypossibleifthemessengerRNAcarryingthecodesurviveslongenoughtobetranslated.Inatypicalcell,anRNAmoleculeisonlystableifspecificallyprotectedfromdegradation.RNAdegradationhasparticularimportanceinregulationofexpressionineukaryoticcellswheremRNAhastotravelsignificantdistancesbeforebeingtranslated.Ineukaryotes,RNAisstabilisedbycertainpost-transcriptionalmodifications,particularlythe5′capandpoly-adenylatedtail. IntentionaldegradationofmRNAisusednotjustasadefencemechanismfromforeignRNA(normallyfromviruses)butalsoasarouteofmRNAdestabilisation.IfanmRNAmoleculehasacomplementarysequencetoasmallinterferingRNAthenitistargetedfordestructionviatheRNAinterferencepathway. ThreeprimeuntranslatedregionsandmicroRNAs[edit] Mainarticle:Threeprimeuntranslatedregion Mainarticle:MicroRNA Threeprimeuntranslatedregions(3′UTRs)ofmessengerRNAs(mRNAs)oftencontainregulatorysequencesthatpost-transcriptionallyinfluencegeneexpression.Such3′-UTRsoftencontainbothbindingsitesformicroRNAs(miRNAs)aswellasforregulatoryproteins.Bybindingtospecificsiteswithinthe3′-UTR,miRNAscandecreasegeneexpressionofvariousmRNAsbyeitherinhibitingtranslationordirectlycausingdegradationofthetranscript.The3′-UTRalsomayhavesilencerregionsthatbindrepressorproteinsthatinhibittheexpressionofamRNA. The3′-UTRoftencontainsmicroRNAresponseelements(MREs).MREsaresequencestowhichmiRNAsbind.Theseareprevalentmotifswithin3′-UTRs.Amongallregulatorymotifswithinthe3′-UTRs(e.g.includingsilencerregions),MREsmakeupabouthalfofthemotifs. Asof2014,themiRBasewebsite,[62]anarchiveofmiRNAsequencesandannotations,listed28,645entriesin233biologicspecies.Ofthese,1,881miRNAswereinannotatedhumanmiRNAloci.miRNAswerepredictedtohaveanaverageofaboutfourhundredtargetmRNAs(affectingexpressionofseveralhundredgenes).[63]Friedmanetal.[63]estimatethat>45,000miRNAtargetsiteswithinhumanmRNA3′UTRsareconservedabovebackgroundlevels,and>60%ofhumanprotein-codinggeneshavebeenunderselectivepressuretomaintainpairingtomiRNAs. DirectexperimentsshowthatasinglemiRNAcanreducethestabilityofhundredsofuniquemRNAs.[64]OtherexperimentsshowthatasinglemiRNAmayrepresstheproductionofhundredsofproteins,butthatthisrepressionoftenisrelativelymild(lessthan2-fold).[65][66] TheeffectsofmiRNAdysregulationofgeneexpressionseemtobeimportantincancer.[67]Forinstance,ingastrointestinalcancers,ninemiRNAshavebeenidentifiedasepigeneticallyalteredandeffectiveindownregulatingDNArepairenzymes.[68] TheeffectsofmiRNAdysregulationofgeneexpressionalsoseemtobeimportantinneuropsychiatricdisorders,suchasschizophrenia,bipolardisorder,majordepression,Parkinson'sdisease,Alzheimer'sdiseaseandautismspectrumdisorders.[69][70] Translationalregulation[edit] Neomycinisanexampleofasmallmoleculethatreducesexpressionofallproteingenesinevitablyleadingtocelldeath;itthusactsasanantibiotic. Mainarticle:Translation(genetics) DirectregulationoftranslationislessprevalentthancontroloftranscriptionormRNAstabilitybutisoccasionallyused.Inhibitionofproteintranslationisamajortargetfortoxinsandantibiotics,sotheycankillacellbyoverridingitsnormalgeneexpressioncontrol.Proteinsynthesisinhibitorsincludetheantibioticneomycinandthetoxinricin. Post-translationalmodifications[edit] Mainarticle:Post-translationalmodification Post-translationalmodifications(PTMs)arecovalentmodificationstoproteins.LikeRNAsplicing,theyhelptosignificantlydiversifytheproteome.Thesemodificationsareusuallycatalyzedbyenzymes.Additionally,processeslikecovalentadditionstoaminoacidsidechainresiduescanoftenbereversedbyotherenzymes.However,some,liketheproteolyticcleavageoftheproteinbackbone,areirreversible.[71] PTMsplaymanyimportantrolesinthecell.[72]Forexample,phosphorylationisprimarilyinvolvedinactivatinganddeactivatingproteinsandinsignalingpathways.[73]PTMsareinvolvedintranscriptionalregulation:animportantfunctionofacetylationandmethylationishistonetailmodification,whichaltershowaccessibleDNAisfortranscription.[71]Theycanalsobeseenintheimmunesystem,whereglycosylationplaysakeyrole.[74]OnetypeofPTMcaninitiateanothertypeofPTM,ascanbeseeninhowubiquitinationtagsproteinsfordegradationthroughproteolysis.[71]Proteolysis,otherthanbeinginvolvedinbreakingdownproteins,isalsoimportantinactivatinganddeactivatingthem,andinregulatingbiologicalprocessessuchasDNAtranscriptionandcelldeath.[75] Measurement[edit] Measuringgeneexpressionisanimportantpartofmanylifesciences,astheabilitytoquantifythelevelatwhichaparticulargeneisexpressedwithinacell,tissueororganismcanprovidealotofvaluableinformation.Forexample,measuringgeneexpressioncan: Identifyviralinfectionofacell(viralproteinexpression). Determineanindividual'ssusceptibilitytocancer(oncogeneexpression). Findifabacteriumisresistanttopenicillin(beta-lactamaseexpression). Similarly,theanalysisofthelocationofproteinexpressionisapowerfultool,andthiscanbedoneonanorganismalorcellularscale.Investigationoflocalizationisparticularlyimportantforthestudyofdevelopmentinmulticellularorganismsandasanindicatorofproteinfunctioninsinglecells.Ideally,measurementofexpressionisdonebydetectingthefinalgeneproduct(formanygenes,thisistheprotein);however,itisofteneasiertodetectoneoftheprecursors,typicallymRNAandtoinfergene-expressionlevelsfromthesemeasurements. mRNAquantification[edit] Thissectiondoesnotciteanysources.Pleasehelpimprovethissectionbyaddingcitationstoreliablesources.Unsourcedmaterialmaybechallengedandremoved.(February2020)(Learnhowandwhentoremovethistemplatemessage) LevelsofmRNAcanbequantitativelymeasuredbynorthernblotting,whichprovidessizeandsequenceinformationaboutthemRNAmolecules.AsampleofRNAisseparatedonanagarosegelandhybridizedtoaradioactivelylabeledRNAprobethatiscomplementarytothetargetsequence.TheradiolabeledRNAisthendetectedbyanautoradiograph.Becausetheuseofradioactivereagentsmakestheproceduretime-consumingandpotentiallydangerous,alternativelabelinganddetectionmethods,suchasdigoxigeninandbiotinchemistries,havebeendeveloped.PerceiveddisadvantagesofNorthernblottingarethatlargequantitiesofRNAarerequiredandthatquantificationmaynotbecompletelyaccurate,asitinvolvesmeasuringbandstrengthinanimageofagel.Ontheotherhand,theadditionalmRNAsizeinformationfromtheNorthernblotallowsthediscriminationofalternatelysplicedtranscripts. AnotherapproachformeasuringmRNAabundanceisRT-qPCR.Inthistechnique,reversetranscriptionisfollowedbyquantitativePCR.ReversetranscriptionfirstgeneratesaDNAtemplatefromthemRNA;thissingle-strandedtemplateiscalledcDNA.ThecDNAtemplateisthenamplifiedinthequantitativestep,duringwhichthefluorescenceemittedbylabeledhybridizationprobesorintercalatingdyeschangesastheDNAamplificationprocessprogresses.Withacarefullyconstructedstandardcurve,qPCRcanproduceanabsolutemeasurementofthenumberofcopiesoforiginalmRNA,typicallyinunitsofcopiespernanolitreofhomogenizedtissueorcopiespercell.qPCRisverysensitive(detectionofasinglemRNAmoleculeistheoreticallypossible),butcanbeexpensivedependingonthetypeofreporterused;fluorescentlylabeledoligonucleotideprobesaremoreexpensivethannon-specificintercalatingfluorescentdyes. Forexpressionprofiling,orhigh-throughputanalysisofmanygeneswithinasample,quantitativePCRmaybeperformedforhundredsofgenessimultaneouslyinthecaseoflow-densityarrays.Asecondapproachisthehybridizationmicroarray.Asinglearrayor"chip"maycontainprobestodeterminetranscriptlevelsforeveryknowngeneinthegenomeofoneormoreorganisms.Alternatively,"tagbased"technologieslikeSerialanalysisofgeneexpression(SAGE)andRNA-Seq,whichcanprovidearelativemeasureofthecellularconcentrationofdifferentmRNAs,canbeused.Anadvantageoftag-basedmethodsisthe"openarchitecture",allowingfortheexactmeasurementofanytranscript,withaknownorunknownsequence.Next-generationsequencing(NGS)suchasRNA-Seqisanotherapproach,producingvastquantitiesofsequencedatathatcanbematchedtoareferencegenome.AlthoughNGSiscomparativelytime-consuming,expensive,andresource-intensive,itcanidentifysingle-nucleotidepolymorphisms,splice-variants,andnovelgenes,andcanalsobeusedtoprofileexpressioninorganismsforwhichlittleornosequenceinformationisavailable. RNAprofilesinWikipedia[edit] TheRNAexpressionprofileoftheGLUT4Transporter(oneofthemainglucosetransportersfoundinthehumanbody) ProfileslikethesearefoundforalmostallproteinslistedinWikipedia.TheyaregeneratedbyorganizationssuchastheGenomicsInstituteoftheNovartisResearchFoundationandtheEuropeanBioinformaticsInstitute.Additionalinformationcanbefoundbysearchingtheirdatabases(foranexampleoftheGLUT4transporterpicturedhere,seecitation).[76]TheseprofilesindicatethelevelofDNAexpression(andhenceRNAproduced)ofacertainproteininacertaintissue,andarecolor-codedaccordinglyintheimageslocatedintheProteinBoxontherightsideofeachWikipediapage. Proteinquantification[edit] Forgenesencodingproteins,theexpressionlevelcanbedirectlyassessedbyanumberofmethodswithsomeclearanalogiestothetechniquesformRNAquantification. OneofthemostcommonlyusedmethodsistoperformaWesternblotagainsttheproteinofinterest.[77]Thisgivesinformationonthesizeoftheproteininadditiontoitsidentity.Asample(oftencellularlysate)isseparatedonapolyacrylamidegel,transferredtoamembraneandthenprobedwithanantibodytotheproteinofinterest.Theantibodycaneitherbeconjugatedtoafluorophoreortohorseradishperoxidaseforimagingand/orquantification.Thegel-basednatureofthisassaymakesquantificationlessaccurate,butithastheadvantageofbeingabletoidentifylatermodificationstotheprotein,forexampleproteolysisorubiquitination,fromchangesinsize. mRNA-proteincorrelation[edit] Whiletranscriptiondirectlyreflectsgeneexpression,thecopynumberofmRNAmoleculesdoesnotdirectlycorrelatewiththenumberofproteinmoleculestranslatedfrommRNA.QuantificationofbothproteinandmRNApermitsacorrelationofthetwolevels.Regulationoneachstepofgeneexpressioncanimpactthecorrelation,asshownforregulationoftranslation[19]orproteinstability.[78]Post-translationalfactors,suchasproteintransportinhighlypolarcells,[79]caninfluencethemeasuredmRNA-proteincorrelationaswell. Localisation[edit] Mainarticles:InsituhybridizationandImmunofluorescence Insitu-hybridizationofDrosophilaembryosatdifferentdevelopmentalstagesforthemRNAresponsiblefortheexpressionofhunchback.HighintensityofbluecolormarksplaceswithhighhunchbackmRNAquantity. Analysisofexpressionisnotlimitedtoquantification;localisationcanalsobedetermined.mRNAcanbedetectedwithasuitablylabelledcomplementarymRNAstrandandproteincanbedetectedvialabelledantibodies.TheprobedsampleisthenobservedbymicroscopytoidentifywherethemRNAorproteinis. Thethree-dimensionalstructureofgreenfluorescentprotein.Theresiduesinthecentreofthe"barrel"areresponsibleforproductionofgreenlightafterexposingtohigherenergeticbluelight.FromPDB:1EMA​. Byreplacingthegenewithanewversionfusedtoagreenfluorescentprotein(orsimilar)marker,expressionmaybedirectlyquantifiedinlivecells.Thisisdonebyimagingusingafluorescencemicroscope.ItisverydifficulttocloneaGFP-fusedproteinintoitsnativelocationinthegenomewithoutaffectingexpressionlevelssothismethodoftencannotbeusedtomeasureendogenousgeneexpression.Itis,however,widelyusedtomeasuretheexpressionofageneartificiallyintroducedintothecell,forexampleviaanexpressionvector.Itisimportanttonotethatbyfusingatargetproteintoafluorescentreportertheprotein'sbehavior,includingitscellularlocalizationandexpressionlevel,canbesignificantlychanged. Theenzyme-linkedimmunosorbentassayworksbyusingantibodiesimmobilisedonamicrotiterplatetocaptureproteinsofinterestfromsamplesaddedtothewell.Usingadetectionantibodyconjugatedtoanenzymeorfluorophorethequantityofboundproteincanbeaccuratelymeasuredbyfluorometricorcolourimetricdetection.ThedetectionprocessisverysimilartothatofaWesternblot,butbyavoidingthegelstepsmoreaccuratequantificationcanbeachieved. Expressionsystem[edit] Tet-ONinducibleshRNAsystem Mainarticle:Proteinproduction(biotechnology) Anexpressionsystemisasystemspecificallydesignedfortheproductionofageneproductofchoice.ThisisnormallyaproteinalthoughmayalsobeRNA,suchastRNAoraribozyme.Anexpressionsystemconsistsofagene,normallyencodedbyDNA,andthemolecularmachineryrequiredtotranscribetheDNAintomRNAandtranslatethemRNAintoproteinusingthereagentsprovided.Inthebroadestsensethisincludeseverylivingcellbutthetermismorenormallyusedtorefertoexpressionasalaboratorytool.Anexpressionsystemisthereforeoftenartificialinsomemanner.Expressionsystemsare,however,afundamentallynaturalprocess.Virusesareanexcellentexamplewheretheyreplicatebyusingthehostcellasanexpressionsystemfortheviralproteinsandgenome. Inducibleexpression[edit] Doxycyclineisalsousedin"Tet-on"and"Tet-off"tetracyclinecontrolledtranscriptionalactivationtoregulatetransgeneexpressioninorganismsandcellcultures. Innature[edit] Inadditiontothesebiologicaltools,certainnaturallyobservedconfigurationsofDNA(genes,promoters,enhancers,repressors)andtheassociatedmachineryitselfarereferredtoasanexpressionsystem.Thistermisnormallyusedinthecasewhereageneorsetofgenesisswitchedonunderwelldefinedconditions,forexample,thesimplerepressorswitchexpressionsysteminLambdaphageandthelacoperatorsysteminbacteria.SeveralnaturalexpressionsystemsaredirectlyusedormodifiedandusedforartificialexpressionsystemssuchastheTet-onandTet-offexpressionsystem. Genenetworks[edit] Mainarticle:Generegulatorynetwork Geneshavesometimesbeenregardedasnodesinanetwork,withinputsbeingproteinssuchastranscriptionfactors,andoutputsbeingthelevelofgeneexpression.Thenodeitselfperformsafunction,andtheoperationofthesefunctionshavebeeninterpretedasperformingakindofinformationprocessingwithincellsanddeterminescellularbehavior. Genenetworkscanalsobeconstructedwithoutformulatinganexplicitcausalmodel.Thisisoftenthecasewhenassemblingnetworksfromlargeexpressiondatasets.[80]Covariationandcorrelationofexpressioniscomputedacrossalargesampleofcasesandmeasurements(oftentranscriptomeorproteomedata).Thesourceofvariationcanbeeitherexperimentalornatural(observational).Thereareseveralwaystoconstructgeneexpressionnetworks,butonecommonapproachistocomputeamatrixofallpair-wisecorrelationsofexpressionacrossconditions,timepoints,orindividualsandconvertthematrix(afterthresholdingatsomecut-offvalue)intoagraphicalrepresentationinwhichnodesrepresentgenes,transcripts,orproteinsandedgesconnectingthesenodesrepresentthestrengthofassociation(seeGeneNetworkGeneNetwork2).[81] Techniquesandtools[edit] Thefollowingexperimentaltechniquesareusedtomeasuregeneexpressionandarelistedinroughlychronologicalorder,startingwiththeolder,moreestablishedtechnologies.Theyaredividedintotwogroupsbasedontheirdegreeofmultiplexity. Low-to-mid-plextechniques: Reportergene Northernblot Westernblot[82] Fluorescentinsituhybridization ReversetranscriptionPCR Higher-plextechniques: SAGE[83] DNAmicroarray[84] Tilingarray[85] RNA-Seq[86] Geneexpressiondatabases[edit] Geneexpressionomnibus(GEO)atNCBI[87] ExpressionAtlasattheEBI MouseGeneExpressionDatabaseattheJacksonLaboratory CollecTF:adatabaseofexperimentallyvalidatedtranscriptionfactor-bindingsitesinBacteria.[88] COLOMBOS:collectionofbacterialexpressioncompendia.[89] ManyMicrobeMicroarraysDatabase:microbialAffymetrixdata[90] Seealso[edit] AlloMapmolecularexpressiontesting Bookmarking Expressedsequencetag ExpressionAtlas Expressionprofiling Genestructure Geneticengineering Geneticallymodifiedorganism Listofbiologicaldatabases Listofhumangenes Oscillatinggene Paramutation Proteinproduction Proteinpurification Ribonomics Ridge Sequenceprofilingtool Transcriptionalbursting Transcriptionalnoise Transcriptofunknownfunction References[edit] ^CrickFH(1958)."Onproteinsynthesis".SymposiaoftheSocietyforExperimentalBiology.12:138–63.PMID 13580867. ^CrickF(August1970)."Centraldogmaofmolecularbiology".Nature.227(5258):561–3.Bibcode:1970Natur.227..561C.doi:10.1038/227561a0.PMID 4913914.S2CID 4164029. ^"Centraldogmareversed".Nature.226(5252):1198–9.June1970.Bibcode:1970Natur.226.1198..doi:10.1038/2261198a0.PMID 5422595.S2CID 4184060. ^TeminHM,MizutaniS(June1970)."RNA-dependentDNApolymeraseinvirionsofRoussarcomavirus".Nature.226(5252):1211–3.doi:10.1038/2261211a0.PMID 4316301.S2CID 4187764. ^BaltimoreD(June1970)."RNA-dependentDNApolymeraseinvirionsofRNAtumourviruses".Nature.226(5252):1209–11.doi:10.1038/2261209a0.PMID 4316300.S2CID 4222378. ^IyerLM,KooninEV,AravindL(January2003)."EvolutionaryconnectionbetweenthecatalyticsubunitsofDNA-dependentRNApolymerasesandeukaryoticRNA-dependentRNApolymerasesandtheoriginofRNApolymerases".BMCStructuralBiology.3:1.doi:10.1186/1472-6807-3-1.PMC 151600.PMID 12553882. ^BruecknerF,ArmacheKJ,CheungA,DamsmaGE,KettenbergerH,LehmannE,SydowJ,CramerP(February2009)."Structure-functionstudiesoftheRNApolymeraseIIelongationcomplex".ActaCrystallographicaD.65(Pt2):112–20.doi:10.1107/S0907444908039875.PMC 2631633.PMID 19171965. ^Krebs,JocelynE.(2017-03-02).Lewin'sgenesXII.Goldstein,ElliottS.,,Kilpatrick,StephenT.Burlington,MA.ISBN 978-1-284-10449-3.OCLC 965781334. ^SirriV,Urcuqui-InchimaS,RousselP,Hernandez-VerdunD(January2008)."Nucleolus:thefascinatingnuclearbody".HistochemistryandCellBiology.129(1):13–31.doi:10.1007/s00418-007-0359-6.PMC 2137947.PMID 18046571. ^FrankDN,PaceNR(1998)."RibonucleaseP:unityanddiversityinatRNAprocessingribozyme".AnnualReviewofBiochemistry.67:153–80.doi:10.1146/annurev.biochem.67.1.153.PMID 9759486. ^CeballosM,VioqueA(2007)."tRNaseZ".ProteinandPeptideLetters.14(2):137–45.doi:10.2174/092986607779816050.PMID 17305600. ^WeinerAM(October2004)."tRNAmaturation:RNApolymerizationwithoutanucleicacidtemplate".CurrentBiology.14(20):R883–5.doi:10.1016/j.cub.2004.09.069.PMID 15498478. ^KöhlerA,HurtE(October2007)."ExportingRNAfromthenucleustothecytoplasm".NatureReviews.MolecularCellBiology.8(10):761–73.doi:10.1038/nrm2255.PMID 17786152.S2CID 10836137. ^JambhekarA,DerisiJL(May2007)."Cis-actingdeterminantsofasymmetric,cytoplasmicRNAtransport".RNA.13(5):625–42.doi:10.1261/rna.262607.PMC 1852811.PMID 17449729. ^AmaralPP,DingerME,MercerTR,MattickJS(March2008)."TheeukaryoticgenomeasanRNAmachine".Science.319(5871):1787–9.Bibcode:2008Sci...319.1787A.doi:10.1126/science.1155472.PMID 18369136.S2CID 206511756. ^HansenTM,BaranovPV,IvanovIP,GestelandRF,AtkinsJF(May2003)."Maintenanceofthecorrectopenreadingframebytheribosome".EMBOReports.4(5):499–504.doi:10.1038/sj.embor.embor825.PMC 1319180.PMID 12717454. ^BerkV,CateJH(June2007)."Insightsintoproteinbiosynthesisfromstructuresofbacterialribosomes".CurrentOpinioninStructuralBiology.17(3):302–9.doi:10.1016/j.sbi.2007.05.009.PMID 17574829. ^SchwanhäusserB,BusseD,LiN,DittmarG,SchuchhardtJ,WolfJ,ChenW,SelbachM(May2011)."Globalquantificationofmammaliangeneexpressioncontrol"(PDF).Nature.473(7347):337–42.Bibcode:2011Natur.473..337S.doi:10.1038/nature10098.PMID 21593866.S2CID 205224972. ^abSchwanhäusserB,BusseD,LiN,DittmarG,SchuchhardtJ,WolfJ,ChenW,SelbachM(March2013)."Corrigendum:Globalquantificationofmammaliangeneexpressioncontrol".Nature.495(7439):126–7.Bibcode:2013Natur.495..126S.doi:10.1038/nature11848.PMID 23407496. ^HegdeRS,KangSW(July2008)."Theconceptoftranslocationalregulation".TheJournalofCellBiology.182(2):225–32.doi:10.1083/jcb.200804157.PMC 2483521.PMID 18644895. ^AlbertsB,JohnsonA,LewisJ,RaffM,RobertsK,WaltersP(2002)."TheShapeandStructureofProteins".MolecularBiologyoftheCell;FourthEdition.NewYorkandLondon:GarlandScience.ISBN 978-0-8153-3218-3. ^AnfinsenCB(July1972)."Theformationandstabilizationofproteinstructure".TheBiochemicalJournal.128(4):737–49.doi:10.1042/bj1280737.PMC 1173893.PMID 4565129. ^JeremyM.Berg,JohnL.Tymoczko,LubertStryer;WebcontentbyNeilD.Clarke(2002)."3.ProteinStructureandFunction".Biochemistry.SanFrancisco:W.H.Freeman.ISBN 978-0-7167-4684-3.{{citebook}}:CS1maint:multiplenames:authorslist(link) ^SelkoeDJ(December2003)."Foldingproteinsinfatalways".Nature.426(6968):900–4.Bibcode:2003Natur.426..900S.doi:10.1038/nature02264.PMID 14685251.S2CID 6451881. ^AlbertsB,BrayD,HopkinK,JohnsonA,LewisJ,RaffM,RobertsK,WalterP(2010)."ProteinStructureandFunction".EssentialCellBiology(3rd ed.).NewYork:GarlandScience,TaylorandFrancisGroup,LLC.pp. 120–170.ISBN 978-0815341291. ^HebertDN,MolinariM(October2007)."InandoutoftheER:proteinfolding,qualitycontrol,degradation,andrelatedhumandiseases".PhysiologicalReviews.87(4):1377–408.doi:10.1152/physrev.00050.2006.PMID 17928587. ^RussellR(January2008)."RNAmisfoldingandtheactionofchaperones".FrontiersinBioscience.13(13):1–20.doi:10.2741/2557.PMC 2610265.PMID 17981525. ^KoberL,ZeheC,BodeJ(April2013)."OptimizedsignalpeptidesforthedevelopmentofhighexpressingCHOcelllines".BiotechnologyandBioengineering.110(4):1164–73.doi:10.1002/bit.24776.PMID 23124363.S2CID 449870. ^MoreauP,BrandizziF,HantonS,ChatreL,MelserS,HawesC,Satiat-JeunemaitreB(2007)."TheplantER-Golgiinterface:ahighlystructuredanddynamicmembranecomplex".JournalofExperimentalBotany.58(1):49–64.doi:10.1093/jxb/erl135.PMID 16990376. ^PrudovskyI,TarantiniF,LandriscinaM,NeivandtD,SoldiR,KirovA,SmallD,KathirKM,RajalingamD,KumarTK(April2008)."SecretionwithoutGolgi".JournalofCellularBiochemistry.103(5):1327–43.doi:10.1002/jcb.21513.PMC 2613191.PMID 17786931. ^ZaidiSK,YoungDW,ChoiJY,PratapJ,JavedA,MontecinoM,SteinJL,LianJB,vanWijnenAJ,SteinGS(October2004)."Intranucleartrafficking:organizationandassemblyofregulatorymachineryforcombinatorialbiologicalcontrol".TheJournalofBiologicalChemistry.279(42):43363–6.doi:10.1074/jbc.R400020200.PMID 15277516. ^MattickJS,AmaralPP,DingerME,MercerTR,MehlerMF(January2009)."RNAregulationofepigeneticprocesses".BioEssays.31(1):51–9.doi:10.1002/bies.080099.PMID 19154003. ^MartinezNJ,WalhoutAJ(April2009)."TheinterplaybetweentranscriptionfactorsandmicroRNAsingenome-scaleregulatorynetworks".BioEssays.31(4):435–45.doi:10.1002/bies.200800212.PMC 3118512.PMID 19274664. ^TomilinNV(April2008)."Regulationofmammaliangeneexpressionbyretroelementsandnon-codingtandemrepeats".BioEssays.30(4):338–48.doi:10.1002/bies.20741.PMID 18348251. ^VeitiaRA(November2008)."Onethousandandonewaysofmakingfunctionallysimilartranscriptionalenhancers".BioEssays.30(11–12):1052–7.doi:10.1002/bies.20849.PMID 18937349. ^NguyenT,NioiP,PickettCB(May2009)."TheNrf2-antioxidantresponseelementsignalingpathwayanditsactivationbyoxidativestress".TheJournalofBiologicalChemistry.284(20):13291–5.doi:10.1074/jbc.R900010200.PMC 2679427.PMID 19182219. ^PaulS(November2008)."Dysfunctionoftheubiquitin-proteasomesysteminmultiplediseaseconditions:therapeuticapproaches".BioEssays.30(11–12):1172–84.doi:10.1002/bies.20852.PMID 18937370.S2CID 29422790. ^LosM,MaddikaS,ErbB,Schulze-OsthoffK(May2009)."SwitchingAkt:fromsurvivalsignalingtodeadlyresponse".BioEssays.31(5):492–5.doi:10.1002/bies.200900005.PMC 2954189.PMID 19319914. ^VerheulTC,vanHijfteL,PerenthalerE,BarakatTS(2020)."TheWhyofYY1:MechanismsofTranscriptionalRegulationbyYinYang1".FrontCellDevBiol.8:592164.doi:10.3389/fcell.2020.592164.PMC 7554316.PMID 33102493. ^SpitzF,FurlongEE(September2012)."Transcriptionfactors:fromenhancerbindingtodevelopmentalcontrol".NatRevGenet.13(9):613–26.doi:10.1038/nrg3207.PMID 22868264.S2CID 205485256. ^abSchoenfelderS,FraserP(August2019)."Long-rangeenhancer-promotercontactsingeneexpressioncontrol".NatRevGenet.20(8):437–455.doi:10.1038/s41576-019-0128-0.PMID 31086298.S2CID 152283312. ^WeintraubAS,LiCH,ZamudioAV,SigovaAA,HannettNM,DayDS,AbrahamBJ,CohenMA,NabetB,BuckleyDL,GuoYE,HniszD,JaenischR,BradnerJE,GrayNS,YoungRA(December2017)."YY1IsaStructuralRegulatorofEnhancer-PromoterLoops".Cell.171(7):1573–1588.e28.doi:10.1016/j.cell.2017.11.008.PMC 5785279.PMID 29224777. ^LambertSA,JolmaA,CampitelliLF,DasPK,YinY,AlbuM,ChenX,TaipaleJ,HughesTR,WeirauchMT(February2018)."TheHumanTranscriptionFactors".Cell.172(4):650–665.doi:10.1016/j.cell.2018.01.029.PMID 29425488. ^GrossmanSR,EngreitzJ,RayJP,NguyenTH,HacohenN,LanderES(July2018)."Positionalspecificityofdifferenttranscriptionfactorclasseswithinenhancers".ProcNatlAcadSciUSA.115(30):E7222–E7230.doi:10.1073/pnas.1804663115.PMC 6065035.PMID 29987030. ^AllenBL,TaatjesDJ(March2015)."TheMediatorcomplex:acentralintegratoroftranscription".NatRevMolCellBiol.16(3):155–66.doi:10.1038/nrm3951.PMC 4963239.PMID 25693131. ^MikhaylichenkoO,BondarenkoV,HarnettD,SchorIE,MalesM,VialesRR,FurlongEE(January2018)."ThedegreeofenhancerorpromoteractivityisreflectedbythelevelsanddirectionalityofeRNAtranscription".GenesDev.32(1):42–57.doi:10.1101/gad.308619.117.PMC 5828394.PMID 29378788. ^LiQJ,YangSH,MaedaY,SladekFM,SharrocksAD,Martins-GreenM(January2003)."MAPkinasephosphorylation-dependentactivationofElk-1leadstoactivationoftheco-activatorp300".EMBOJ.22(2):281–91.doi:10.1093/emboj/cdg028.PMC 140103.PMID 12514134. ^CarulloNV,PhillipsIRA,SimonRC,SotoSA,HindsJE,SalisburyAJ,RevannaJS,BunnerKD,IanovL,SultanFA,SavellKE,GersbachCA,DayJJ(September2020)."EnhancerRNAspredictenhancer-generegulatorylinksandarecriticalforenhancerfunctioninneuronalsystems".NucleicAcidsRes.48(17):9550–9570.doi:10.1093/nar/gkaa671.PMC 7515708.PMID 32810208. ^LövkvistC,DoddIB,SneppenK,HaerterJO(June2016)."DNAmethylationinhumanepigenomesdependsonlocaltopologyofCpGsites".NucleicAcidsResearch.44(11):5123–32.doi:10.1093/nar/gkw124.PMC 4914085.PMID 26932361. ^JabbariK,BernardiG(May2004)."CytosinemethylationandCpG,TpG(CpA)andTpAfrequencies".Gene.333:143–9.doi:10.1016/j.gene.2004.02.043.PMID 15177689. ^WeberM,HellmannI,StadlerMB,RamosL,PääboS,RebhanM,SchübelerD(April2007)."Distribution,silencingpotentialandevolutionaryimpactofpromoterDNAmethylationinthehumangenome".Nat.Genet.39(4):457–66.doi:10.1038/ng1990.PMID 17334365.S2CID 22446734. ^YangX,HanH,DeCarvalhoDD,LayFD,JonesPA,LiangG(October2014)."Genebodymethylationcanaltergeneexpressionandisatherapeutictargetincancer".CancerCell.26(4):577–90.doi:10.1016/j.ccr.2014.07.028.PMC 4224113.PMID 25263941. ^MaederML,AngstmanJF,RichardsonME,LinderSJ,CascioVM,TsaiSQ,HoQH,SanderJD,ReyonD,BernsteinBE,CostelloJF,WilkinsonMF,JoungJK(December2013)."TargetedDNAdemethylationandactivationofendogenousgenesusingprogrammableTALE-TET1fusionproteins".Nat.Biotechnol.31(12):1137–42.doi:10.1038/nbt.2726.PMC 3858462.PMID 24108092. ^KimJJ,JungMW(2006)."NeuralcircuitsandmechanismsinvolvedinPavlovianfearconditioning:acriticalreview".NeuroscienceandBiobehavioralReviews.30(2):188–202.doi:10.1016/j.neubiorev.2005.06.005.PMC 4342048.PMID 16120461. ^abDukeCG,KennedyAJ,GavinCF,DayJJ,SweattJD(July2017)."Experience-dependentepigenomicreorganizationinthehippocampus".Learning&Memory.24(7):278–288.doi:10.1101/lm.045112.117.PMC 5473107.PMID 28620075. ^abBernsteinC(2022)."DNAMethylationandEstablishingMemory".EpigenetInsights.15:25168657211072499.doi:10.1177/25168657211072499.PMC 8793415.PMID 35098021. ^abKeiferJ(February2017)."PrimetimeforLearningGenes".Genes(Basel).8(2):69.doi:10.3390/genes8020069.PMC 5333058.PMID 28208656. ^SaxonovS,BergP,BrutlagDL(January2006)."Agenome-wideanalysisofCpGdinucleotidesinthehumangenomedistinguishestwodistinctclassesofpromoters".ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica.103(5):1412–7.Bibcode:2006PNAS..103.1412S.doi:10.1073/pnas.0510310103.PMC 1345710.PMID 16432200. ^BirdA(January2002)."DNAmethylationpatternsandepigeneticmemory".Genes&Development.16(1):6–21.doi:10.1101/gad.947102.PMID 11782440. ^VogelsteinB,PapadopoulosN,VelculescuVE,ZhouS,DiazLA,KinzlerKW(March2013)."Cancergenomelandscapes".Science.339(6127):1546–58.Bibcode:2013Sci...339.1546V.doi:10.1126/science.1235122.PMC 3749880.PMID 23539594. ^TessitoreA,CicciarelliG,DelVecchioF,GaggianoA,VerzellaD,FischiettiM,VecchiottiD,CapeceD,ZazzeroniF,AlesseE(2014)."MicroRNAsintheDNADamage/RepairNetworkandCancer".InternationalJournalofGenomics.2014:1–10.doi:10.1155/2014/820248.PMC 3926391.PMID 24616890. ^miRBase.org ^abFriedmanRC,FarhKK,BurgeCB,BartelDP(January2009)."MostmammalianmRNAsareconservedtargetsofmicroRNAs".GenomeResearch.19(1):92–105.doi:10.1101/gr.082701.108.PMC 2612969.PMID 18955434. ^LimLP,LauNC,Garrett-EngeleP,GrimsonA,SchelterJM,CastleJ,BartelDP,LinsleyPS,JohnsonJM(February2005)."MicroarrayanalysisshowsthatsomemicroRNAsdownregulatelargenumbersoftargetmRNAs".Nature.433(7027):769–73.Bibcode:2005Natur.433..769L.doi:10.1038/nature03315.PMID 15685193.S2CID 4430576. ^SelbachM,SchwanhäusserB,ThierfelderN,FangZ,KhaninR,RajewskyN(September2008)."WidespreadchangesinproteinsynthesisinducedbymicroRNAs".Nature.455(7209):58–63.Bibcode:2008Natur.455...58S.doi:10.1038/nature07228.PMID 18668040.S2CID 4429008. ^BaekD,VillénJ,ShinC,CamargoFD,GygiSP,BartelDP(September2008)."TheimpactofmicroRNAsonproteinoutput".Nature.455(7209):64–71.Bibcode:2008Natur.455...64B.doi:10.1038/nature07242.PMC 2745094.PMID 18668037. ^PalmeroEI,deCamposSG,CamposM,deSouzaNC,GuerreiroID,CarvalhoAL,MarquesMM(July2011)."MechanismsandroleofmicroRNAderegulationincanceronsetandprogression".GeneticsandMolecularBiology.34(3):363–70.doi:10.1590/S1415-47572011000300001.PMC 3168173.PMID 21931505. ^BernsteinC,BernsteinH(May2015)."EpigeneticreductionofDNArepairinprogressiontogastrointestinalcancer".WorldJournalofGastrointestinalOncology.7(5):30–46.doi:10.4251/wjgo.v7.i5.30.PMC 4434036.PMID 25987950. ^MelliosN,SurM(2012)."TheEmergingRoleofmicroRNAsinSchizophreniaandAutismSpectrumDisorders".FrontiersinPsychiatry.3:39.doi:10.3389/fpsyt.2012.00039.PMC 3336189.PMID 22539927. ^GeaghanM,CairnsMJ(August2015)."MicroRNAandPosttranscriptionalDysregulationinPsychiatry".BiologicalPsychiatry.78(4):231–9.doi:10.1016/j.biopsych.2014.12.009.PMID 25636176. ^abcWalshCT,Garneau-TsodikovaS,GattoGJ(December2005)."Proteinposttranslationalmodifications:thechemistryofproteomediversifications".AngewandteChemie.44(45):7342–72.doi:10.1002/anie.200501023.PMID 16267872.S2CID 32157563. ^KhouryGA,BalibanRC,FloudasCA(September2011)."Proteome-widepost-translationalmodificationstatistics:frequencyanalysisandcurationoftheswiss-protdatabase".ScientificReports.1(90):90.Bibcode:2011NatSR...1E..90K.doi:10.1038/srep00090.PMC 3201773.PMID 22034591. ^MannM,JensenON(March2003)."Proteomicanalysisofpost-translationalmodifications".NatureBiotechnology.21(3):255–61.doi:10.1038/nbt0303-255.PMID 12610572.S2CID 205266061. ^SeoJ,LeeKJ(January2004)."Post-translationalmodificationsandtheirbiologicalfunctions:proteomicanalysisandsystematicapproaches".JournalofBiochemistryandMolecularBiology.37(1):35–44.doi:10.5483/bmbrep.2004.37.1.035.PMID 14761301. ^RogersLD,OverallCM(December2013)."Proteolyticpost-translationalmodificationofproteins:proteomictoolsandmethodology".Molecular&CellularProteomics.12(12):3532–42.doi:10.1074/mcp.M113.031310.PMC 3861706.PMID 23887885. ^"Searchresults