Chapter21RegulationofTranscription21.1Introduction

21.2Responseelementsidentifygenesundercommonregulation

21.3TherearemanytypesofDNA-bindingdomains

21.4AzincfingermotifisaDNA-bindingdomain

21.5Steroidreceptorsaretranscriptionfactors

21.6Steroidreceptorshavezincfingers

21.7Bindingtotheresponseelementisactivatedbyligand-binding

21.8Steroidreceptorsrecognizeresponseelementsbyacombinatorialcode

21.9HomeodomainsbindrelatedtargetsinDNA

21.10Helix-loop-helixproteinsinteractbycombinatorialassociation

21.11Leucinezippersareinvolvedindimerformation

21.12Transcriptioninitiationrequireschangesinchromatinstructure

21.13Chromatinremodelingisanactiveprocess

21.14Activationoftranscriptionrequireschangesinnucleosomeorganizationatthepromoter

21.15Histoneacetylationanddeacetylationcontrolchromatinactivity

21.16Polycombandtrithoraxareantagonisticrepressorsandactivators

21.17AnLCRmaycontroladomain

21.18Insulatorsblockenhanceractions

21.19Insulatorscanvaryinstrength

21.20Adomainhasseveraltypesofelements

21.21Geneexpressionisassociatedwithdemethylation

21.22CpGislandsareregulatorytargetsActivationofgenestructure

Initiationoftranscription

Processingthetranscript

Transporttocytoplasm

TranslationofmRNA21.1IntroductionTable21.1Incucibletranscriptionfactorsbindtoresponseelementsthatidentifygroupsofpromotersorenhancerssubjecttocoordinatecontrol.21.2ResponseelementsidentifygenesundercommonregulationRegulatoryAgentModuleConsensusFactorHeatshockHSECNNGAANNTCCNNGHSTFGlucocorticoidGRETGGTACAAATGTTCTReceptorPhorbolesterTRETGACTCAAP1SerumSRECCATATTAGGSRFFigure21.1Theregulatoryregionofahumanmetallothioneingenecontainsregulatorelementsinbothitspromoterandenhancer.Thepromoterhaselementsformetalinduction;anenhancerhasanelementforresponsetoglucocorticoid.Promoterelementsareshownabovethemap,andproteinsthatbindthemareindicatedbelow.

21.2ResponseelementsidentifygenesundercommonregulationFigure21.2Theactivityofaregulatorytranscriptionfactormaybecontrolledbysynthesisofprotein,covalentmodificationofprotein,ligandbinding,orbindingofinhibitorsthatsequestertheproteinoraffectitsabilitytobindtoDNA.21.3TherearemanytypesofDNA-bindingdomains

Figure28.19Oncogenesthatcodefortranscriptionfactorshavemutationsthatinactivatetranscription(v-erbAandpossiblyv-rel)orthatactivatetranscription(v-junandv-fos).21.3TherearemanytypesofDNA-bindingdomains

Figure21.3TranscriptionfactorSP1hasaseriesofthreezincfingers,eachwithacharacteristicpatternofcysteineandhistidineresiduesthatconstitutethezinc-bindingsite.21.4AzincfingermotifisaDNA-bindingdomainFigure21.4Zincfingersmayforma-helicesthatinsertintothemajorgroove,associatedwithb-sheetsontheotherside.21.4AzincfingermotifisaDNA-bindingdomainFigure21.5ThefirstfingerofasteroidreceptorcontrolsspecificityofDNA-binding(positionsshowninred);thesecondfingercontrolsspecificityofdimerization(positionsshowninblue).TheexpandedviewofthefirstfingershowsthatdiscriminationbetweenGREandEREtargetsequencesrestsontwoaminoacidsatthebase.21.4AzincfingermotifisaDNA-bindingdomainReceptorisatransmembraneprotein,locatedintheplasmamembrane,thatbindsaligandinadomainontheextracellularside,andasaresulthasachangeinactivityofthecytoplasmicdomain.(Thesametermissometimesusedalsoforthesteroidreceptors,whicharetranscriptionfactorsthatareactivatedbybindingligandsthataresteroidsorothersmallmolecules.)21.5Steroidreceptorshaveseveralindependentdomains

Figure21.6Severaltypesofhydrophobicsmallmoleculesactivatetranscriptionfactors.Corticoidsandsteroidsexhormonesaresynthesizedfromcholesterol,vitaminDisasteroid,thyroidhormonesaresynthesizedfromtyrosine,andretinoicacidissynthesizedfromisoprene(infishliver).21.5SteroidreceptorshaveseveralindependentdomainsFigure21.7Glucocorticoidsregulategenetranscriptionbycausingtheirreceptortobindtoanenhancerwhoseactionisneededforpromoterfunction.

21.5SteroidreceptorshaveseveralindependentdomainsFigure21.8Receptorsformanysteroidandthyroidhormoneshaveasimilarorganization,withanindividualN-terminalregion,conservedDNA-bindingregion,andaC-terminalhormone-bindingregion.21.5SteroidreceptorshaveseveralindependentdomainsFigure21.8Receptorsformanysteroidandthyroidhormoneshaveasimilarorganization,withanindividualN-terminalregion,conservedDNA-bindingregion,andaC-terminalhormone-bindingregion.21.5SteroidreceptorshaveseveralindependentdomainsFigure21.5ThefirstfingerofasteroidreceptorcontrolsspecificityofDNA-binding(positionsshowninred);thesecondfingercontrolsspecificityofdimerization(positionsshowninblue).TheexpandedviewofthefirstfingershowsthatdiscriminationbetweenGREandEREtargetsequencesrestsontwoaminoacidsatthebase.21.5SteroidreceptorshaveseveralindependentdomainsFigure21.19CoactivatorsmayhaveHATactivitiesthatacetylatethetailsofnucleosomalhistones.

21.5SteroidreceptorshaveseveralindependentdomainsFigure21.20Arepressorcomplexcontainsthreecomponents:aDNAbindingsubunit,acorepressor,andahistonedeacetylase.21.5SteroidreceptorshaveseveralindependentdomainsFigure21.9TRandRARbindtheSMRTcorepressorintheabsenceofligand.Thepromoterisnotexpressed.WhenSMRTisdisplacedbybindingofligand,thereceptorbindsacoactivatorcomplex.Thisleadstoactivationoftranscriptionbythebasalapparatus.21.5SteroidreceptorshaveseveralindependentdomainsFigure21.10ThehomeodomainmaybethesoleDNA-bindingmotifinatranscriptionalregulatorormaybecombinedwithothermotifs.Itrepresentsadiscrete(60residue)partoftheprotein.21.6HomeodomainsbindrelatedtargetsinDNAFigure21.11ThehomeodomainoftheAntennapediagenerepresentsthemajorgroupofgenescontaininghomeoboxesinDrosophila;engrailed(en)representsanothertypeofhomeoticgene;andthemammalianfactorOct-2representsadistantlyrelatedgroupoftranscriptionfactors.Thehomeodomainisconventionallynumberedfrom1to60.ItstartswiththeN-terminalarm,andthethreehelicalregionsoccupyresidues10-22,28-38,and42-58.21.6HomeodomainsbindrelatedtargetsinDNAFigure21.12Helix3ofthehomeodomainbindsinthemajorgrooveofDNA,withhelices1and2lyingoutsidethedoublehelix.Helix3contactsboththephosphatebackboneandspecificbases.TheN-terminalarmliesintheminorgroove,andmakesadditionalcontacts.

21.6HomeodomainsbindrelatedtargetsinDNAFigure29.8Theposteriorpathwayhastwobranches,responsibleforabdominaldevelopmentandgermcellformation.21.6HomeodomainsbindrelatedtargetsinDNAFigure21.13AllHLHproteinshaveregionscorrespondingtohelix1andhelix2,separatedbyaloopof10-24residues.BasicHLHproteinshavearegionwithconservedpositivechargesimmediatelyadjacenttohelix1.

21.7Helix-loop-helixproteinsinteractbycombinatorialassociation

Figure21.14AnHLHdimerinwhichbothsubunitsareofthebHLHtypecanbindDNA,butadimerinwhichonesubunitlacksthebasicregioncannotbindDNA.21.7Helix-loop-helixproteinsinteractbycombinatorialassociation

Figure21.15ThebasicregionsofthebZIPmotifareheldtogetherbythedimerizationattheadjacentzipperregionwhenthehydrophobicfacesoftwoleucinezippersinteractinparallelorientation.21.8LeucinezippersareinvolvedindimerformationFigure20.19Anenhancercontainsseveralstructuralmotifs.Thehistogramplotstheeffectofallmutationsthatreduceenhancerfunctionto<75%ofwildtype.Bindingsitesforproteinsareindicatedbelowthehistogram.21.8LeucinezippersareinvolvedindimerformationChromatinremodelingdescribestheenergy-dependentdisplacementorreorganizationofnucleosomesthatoccursinconjunctionwithactivationofgenesfortranscription.21.9Chromatinremodelingisanactiveprocess

Figure21.16Thepre-emptivemodelfortranscriptionofchromatinproposesthatifnucleosomesformatapromoter,transcriptionfactors(andRNApolymerase)cannotbind.Iftranscriptionfactors(andRNApolymerase)bindtothepromotertoestablishastablecomplexforinitiation,histonesareexcluded.21.9ChromatinremodelingisanactiveprocessFigure21.17ThedynamicmodelfortranscriptionofchromatinreliesuponfactorsthatcanuseenergyprovidedbyhydrolysisofATPtodisplacenucleosomesfromspecificDNAsequences.21.9ChromatinremodelingisanactiveprocessFigure21.18HormonereceptorandNF1cannotbindsimultaneouslytotheMMTVpromoterintheformoflinearDNA,butcanbindwhentheDNAispresentedonanucleosomalsurface.21.9ChromatinremodelingisanactiveprocessFigure21.18HormonereceptorandNF1cannotbindsimultaneouslytotheMMTVpromoterintheformoflinearDNA,butcanbindwhentheDNAispresentedonanucleosomalsurface.21.9ChromatinremodelingisanactiveprocessHAT(histoneacetyltransferase)enzymesmodifyhistonesbyadditionofacetylgroups;sometranscriptionalcoactivatorshaveHATactivity.

HDAC(histonedeacetyltransferase)enzymesremoveacetylgroupsfromhistones;theymaybeassociatedwithrepressorsoftranscription.21.10Histoneacetylationanddeacetylationcontrolchromatinactivity

Figure20.26Anupstreamtranscriptionfactormaybindacoactivatorthatcontactsthebasalapparatus.21.10HistoneacetylationanddeacetylationcontrolchromatinactivityFigure21.19CoactivatorsmayhaveHATactivitiesthatacetylatethetailsofnucleosomalhistones.21.10HistoneacetylationanddeacetylationcontrolchromatinactivityFigure21.20Arepressorcomplexcontainsthreecomponents:aDNAbindingsubunit,acorepressor,andahistonedeacetylase.21.10HistoneacetylationanddeacetylationcontrolchromatinactivityFigure21.21Pc-Gproteinsdonotinitiaterepression,butareresponsibleformaintainingit.21.11PolycombandtrithoraxareantagonisticrepressorsandactivatorsFigure19.45Extensionofheterochromatininactivatesgenes.Theprobabilitythatagenewillbeinactivateddependsonitsdistancefromtheheterochromatinregion.21.11PolycombandtrithoraxareantagonisticrepressorsandactivatorsDomainofachromosomemayrefereithertoadiscretestructuralentitydefinedasaregionwithinwhichsupercoilingisindependentofotherdomains;ortoanextensiveregionincludinganexpressedgenethathasheightenedsensitivitytodegradationbytheenzymeDNAaseI.

MAR(matrixattachmentsite;alsoknownasSARforscaffoldattachmentsite)isaregionofDNAthatattachestothenuclearmatrix.21.12Longrangeregulationandinsulationofdomains

Figure4.1Eachofthea-likeandb-likeglobingenefamiliesisorganizedintoasingleclusterthatincludesfunctionalgenesandpseudogenes(y).

21.12Longrangeregulationandinsulationofdomains

Figure4.1Eachofthea-likeandb-likeglobingenefamiliesisorganizedintoasingleclusterthatincludesfunctionalgenesandpseudogenes(y).

21.12Longrangeregulationandinsulationofdomains

Figure21.22Aglobindomainismarkedbyhypersensitivesitesateitherend.Thegroupofsitesatthe5￠sideconstitutestheLCRandisessentialforthefunctionofallgenesinthecluster.21.12Longrangeregulationandinsulationofdomains

Figure19.42SensitivitytoDNAaseIcanbemeasuredbydeterminingtherateofdisappearanceofthematerialhybridizingwithaparticularprobe.21.12Longrangeregulationandinsulationofdomains

Figure21.23SpecializedchromatinstructuresthatincludehypersensitivesitesmarktheendsofadomainintheD.melanogastergenomeandinsulategenesbetweenthemfromtheeffectsofsurroundingsequences.

21.12Longrangeregulationandinsulationofdomains

Figure21.24Aproteinthatbindstotheinsulatorscs￠islocalizedatinterbandsinDrosophilapolytenechromosomes.RedstainingidentifiestheDNA(thebands)onboththeupperandlowersamples;greenstainingidentifiesBEAF32(oftenatinterbands)ontheuppersample.Yellowshowscoincidenceofthetwolabels.Someofthemoreprominentstainedinterbandsaremarkedbywhitelines.PhotographkindlyprovidedbyUliLaemmli.21.12Longrangeregulationandinsulationofdomains

Figure21.25Theinsulatorofthegypsytransposonblockstheactionofanenhancerwhenitisplacedbetweentheenhancerandthepromoter.

21.12Longrangeregulationandinsulationofdomains

Figure29.32ThehomeoticgenesoftheANT-Ccomplexconferidentityonthemostanteriorsegmentsofthefly.Thegenesvaryinsize,andareinterspersedwithothergenes.Theantpgeneisverylargeandhasalternativeformsofexpression.21.12Longrangeregulationandinsulationofdomains

Figure21.26Fab-7isaboundaryelementthatisnecessaryfortheindependenceofregulatoryelementsiab-6andiab-7.21.12Longrangeregulationandinsulationofdomains

Figure21.27Domainsmaypossessthreetypesofsites:insulatorstopreventeffectsfromspreadingbetweendomains;MARstoattachthedomaintothenuclearmatrix;andLCRsthatarerequiredforinitiationoftranscription.21.12Longrangeregulationandinsulationofdomains

Figure21.28TherestrictionenzymeMspIcleavesallCCGGsequenceswhetherornottheyaremethylatedatthesecondC,butHpaIIcleavesonlynonmethylatedCCGGtetramers.21.13GeneexpressionisassociatedwithdemethylationFigure21.29TheresultsofMspIandHpaIIcleavagearecomparedbygelelectrophoresisofthefragments.

21.13GeneexpressionisassociatedwithdemethylationFigure13.30ReplicationofmethylatedDNAgiveshemimethylatedDNA,whichmaintainsitsstateatGATCsitesuntiltheDammethylaserestoresthefullymethylatedcondition.21.13GeneexpressionisassociatedwithdemethylationFigure21.30ThetypicaldensityofCpGdoubletsinmammalianDNAis~1/100bp,asseenforag-globingene.InaCpG-richisland,thedensityisincreasedto>10doublets/100bp.TheislandintheAPRTgenestarts~100bpupstreamofthepromoterandextends~400bpintothegene.EachverticallinerepresentsaCpGdoublet.21.13GeneexpressionisassociatedwithdemethylationFigure21.20Arepressorcomplexcontainsthreecomponents:aDNAbindingsubunit,acorepressor,andahistonedeacetylase.21.13