Gene-X-ppt(Gene10-基因十)--Chapter10

Chapter10Chromatin10.1Introduction•nucleosome–Thebasicstructuralsubunitofchromatin,consistingof~200bpofDNAandanoctamerofhistoneproteins.•histonetails–Flexibleamino-orcarboxy-terminalregionsofthecorehistonesthatextendbeyondthesurfaceofthenucleosome.–Histonetailsaresitesofextensiveposttranslationalmodification.10.1Introduction•10nmfiber–Alineararrayofnucleosomesgeneratedbyunfoldingfromthenaturalconditionofchromatin.•linkerhistones–Afamilyofhistones(suchashistoneH1)thatarenotcomponentsofthenucleosomecore.–Linkerhistonesbindnucleosomesand/orlinkerDNAandpromote30nmfiberformation.10.1Introduction•30nmfiber–Acoilofnucleosomes.–Itisthebasicleveloforganizationofnucleosomesinchromatin.•nonhistone–Anystructuralproteinfoundinachromosomeexceptoneofthehistones.10.2DNAIsOrganizedinArraysofNucleosomes•MNasecleaveslinkerDNAandreleasesindividualnucleosomesfromchromatin.•95%oftheDNAisrecoveredinnucleosomesormultimerswhenMNasecleavesDNAinchromatin.•ThelengthofDNApernucleosomevariesforindividualtissuesorspeciesinarangefrom154to260bp.•NucleosomalDNAisdividedintothecoreDNAandlinkerDNAdependingonitssusceptibilitytoMNase.ReprintedfromCell,vol.4,P.Oudet,M.Gross-Bellard,andP.Chambon,Electronmicroscopicandbiochemicalevidence...,pp.281-300.Copyright1975,withpermissionfromElsevier[].PhotocourtesyofPierreChambon,CollegeofFrance.FIGURE02:Individualnucleosomesarereleasedbydigestionofchromatinwithmicrococcalnuclease.Thebaris100nm.10.2DNAIsOrganizedinArraysofNucleosomes•ThecoreDNAisthelengthof146bpthatisfoundonthecoreparticlesproducedbyprolongeddigestionwithMNase.•LinkerDNAistheregionof8to114bpthatissusceptibletoearlycleavagebynucleases.FIGURE05:Micrococcalnucleaseinitiallycleavesbetweennucleosomes10.3TheNucleosomeIstheSubunitofAllChromatin•Anucleosomecontains~200bpofDNAandtwocopiesofeachcorehistone(H2A,H2B,H3,andH4).•DNAiswrappedaroundtheoutsidesurfaceoftheproteinoctamer.•ThehistoneoctamerhasastructureofanH32-H42tetramerassociatedwithtwoH2A-H2Bdimers.FIGURE06:ThenucleosomeconsistsofapproximatelyequalmassesofDNAandhistones(includingH1)10.3TheNucleosomeIstheSubunitofAllChromatin10.3TheNucleosomeIstheSubunitofAllChromatinFIGURE07:ThenucleosomeisacylinderwithDNAorganizedinto~12/3turnsaroundthesurface10.3TheNucleosomeIstheSubunitofAllChromatin•Eachhistoneisextensivelyinterdigitatedwithitspartner.•Allcorehistoneshavethestructuralmotifofthehistonefold.N-andC-terminalhistonetailsextendoutofthenucleosome.•H1isassociatedwithlinkerDNAandmaylieatthepointwhereDNAentersorexitsthenucleosome.PhotoscourtesyofE.N.Moudrianakis,JohnsHopkinsUniversity.FIGURE10ab:Thecrystalstructureofthehistonecoreoctamerisrepresentedinaspace-fillingmodel10.3TheNucleosomeIstheSubunitofAllChromatinFIGURE11a:Thehistonefoldconsistsoftwoshorta-helicesflankingalongera-helixFIGURE11b:Histonepairs(H3+H4andH2A+H2B)interacttoformhistonedimersStructuresfromProteinDataBank1HIO.G.Arents,etal.,Proc.Natl.Acad.Sci.USA88(1991):10145-10152.10.3TheNucleosomeIstheSubunitofAllChromatinFIGURE13:Thehistonefolddomainsofthehistonesarelocatedinthecoreofthenucleosome10.4NucleosomesAreCovalentlyModified•Histonesaremodifiedbymethylation,acetylation,phosphorylation,andothermodifications.•Combinationsofspecifichistonemodificationsdefinethefunctionoflocalregionsofchromatin;thisisknownasthehistonecode.FIGURE16:HistonetailshavemanysitesofmodificationAdaptedfromTheScientist17(2003):p.27.10.4NucleosomesAreCovalentlyModified•Thebromodomainisfoundinavarietyofproteinsthatinteractwithchromatin.–Itisusedtorecognizeacetylatedsitesonhistones.FIGURE21:BromodomainsareproteinmotifsthatbindacetyllysinesStructurefromProteinDataBank1E6I.D.J.Owen,etal.,EMBOJ.19(2000):6141-6149.10.4NucleosomesAreCovalentlyModified•Severalproteinmotifsrecognizemethyllysines,suchaschromodomains,PHDdomains,andTudordomains.FIGURE22:NumerousproteinmotifsrecognizemethylatedlysinesStructurefromProteinDataBank1KNE.S.A.JacobsandS.Khorasanizadeh,Science295(2002):2080-2083.StructurefromProteinDataBank2GFA.Y.Huang,etal.,Science12(2006):748-751.10.4NucleosomesAreCovalentlyModifiedPhotocourtesyofSeanD.Taverna,JohnsHopkinsUniversitySchoolofMedicine,andHaitaoLi,MemorialSloan-KetteringCancerCenter.AdditionalinformationatS.D.Taverna,etal.,Nat.Struct.Mol.Biol.14(2007):1025-1040.FIGURE22c:Numerousproteinmotifsrecognizemethylatedlysines10.4NucleosomesAreCovalentlyModifiedFIGURE18:Acetylationduringreplicationoccursonspecificsitesonhistonesbeforetheyareincorporatedintonucleosomes10.4NucleosomesAreCovalentlyModifiedFIGURE19:Acetylationassociatedwithgeneactivationoccursbydirectlymodifyingspecificsitesonhistonesthatarealreadyincorporatedintonucleosomes10.5HistoneVariantsProduceAlternativeNucleosomes•AllcorehistonesexceptH4aremembersoffamiliesofrelatedvariants.•Histonevariantscanbecloselyrelatedorhighlydivergentfromcanonicalhistones.•Differentvariantsservedifferentfunctionsinthecell.10.5HistoneVariantsProduceAlternativeNucleosomesFIGURE23:Themajorcorehistonescontainaconservedhistone-folddomainAdaptedfromK.SarmaandD.Re