05 基因组与染色体.ppt

Chapter5Genomeandchromosome 5 1Genomesize 5 2Eukaryoticgenomes 5 3Eukaryoticgenes 5 4PackageofEukaryoticgenomes 5 5Prokaryoticgenomesandpackage 5 6GenomeCharacteristicsofAnimalVirus Chromatin describestheconditionofthechromosomalmaterialduringtheinterphase betweenmitoses ofthecellcycle Chromosome isadiscreteunitofthegenomecarryingmanygenes EachchromosomeconsistsofaverylongmoleculeofduplexDNAandanapproximatelyequalmassofproteins Itisvisibleasamorphologicalentityonlyduringcelldivision Nucleoid isthecompactbodythatcontainsthegenomeinabacterium 5 1 Genomesizeandchromosome Keyterms TranscriptomeisthecompletesetofmRNAspresentinacell tissue ororganism Proteomeisthetotalnumberofproteinsproducedbyanorganism Genomeisthecompletesetofsequencesinthegeneticmaterialofanorganism ItincludesthesequenceofeachchromosomeplusanyDNAinorganelles 1 C valueThetotalamountofDNAinthe haploid genomeisacharacteristicofeachlivingspeciesknownasitsC value ThereisenormousvariationintherangeofC values from1011bpforsomeplantsandamphibians TherangeofDNAvalueswithinaphylumisindicatedbytheshadedarea 开花植物鸟类哺乳动物爬行动物两栖动物硬骨鱼软骨鱼棘皮动物甲壳动物昆虫软体动物蠕虫霉菌藻类真菌G G 支原体 DNAcontentofthehaploidgenomeC valueisrelatedtothemorphologicalcomplexityoflowereukaryotes butvariesextensivelyamongthehighereukaryotes Thegenomesizesofsomecommonexperimentalorganisms 藻类粘菌线虫 Conclusions Wecanseethesteadyincreaseingenomesizewithmorphologicalcomplexityinsomeofthemostcommonlyanalyzedorganisms Asweclimbtheevolutionarytree however therelationshipbetweenmorphologicalcomplexityoftheorganismandcontentofDNAbecomesobscure Buttherearesomeextremelycuriousvariationsinrelativegenomesize ForExample ThetoadXenopus 蟾蜍 andmanhavegenomesofessentiallythesamesize AndinsomephylathereareextremelylargevariationsinDNAcontentbetweenorganismsthatdonotvarymuchinmorphologicalcomplexitysuchasamphibians andplants Inamphibians thesmallestgenomesare 109bp whilethelargestare 1011bp Thereisunlikelytobealargedifferenceinthenumberofgenesneededtospecifytheseamphibians Why 2 C valueparadoxItreferstothelackofacorrelationbetweengenomesizeandgeneticcomplexity ThereisanexcessofDNAcomparedwiththeamountthatcouldbeexpectedtocodeforprotein TherearelargevariationsinC valuesbetweencertainspecieswhoseapparentcomplexitydoesnotvarymuch Twopuzzlingfeatures Thesequestionscanbedirectlyansweredbygenomesequences butatpresentwehavedirectinformationforonlyafewindividualgenomes 5 2Eukaryoticgenomes Severalsequencecomponentsineukaryoticgenomes NonrepetitiveDNAconsistsofsequencesthatareunique thereisonlyonecopyinahaploidgenome RepetitiveDNAdescribessequencesthatarepresentinmorethanonecopyineachgenome RepetitiveDNAisoftenclassedintotwogeneraltypes Moderatelyrepetitive 10 几百个Highlyrepetitive 几百 几百万个InvertedrepetitiveDNA ThelengthofthenonrepetitiveDNAcomponenttendstoincreasewithoverallgenomesize sometimesthoseof2 3copiesarealsocallednonrepetitiveDNA ThenonrepetitiveDNAcontentofgenomesthereforeaccordsbetterwithoursenseoftherelativecomplexityoftheorganism Forexample E coli4 2 106bpC elegans6 6 107bpD melanogaster 108bpmammals 2 109bp Furtherincreaseingenomesize however generallyreflectsanincreaseintheamountandproportionoftherepetitivecomponents 1 NonrepetitiveDNA Theproportionsofdifferentsequencecomponentsvaryineukaryoticgenomes TheabsolutecontentofnonrepetitiveDNAincreaseswithgenomesize butreachesaplateauat 2 109bp 2 Moderatelyrepetitive ModeratelyrepetitiveDNAconsistsofrelativelyshortsequencesthatarerepeatedtypically300 1000bpinthegenome Thesequencesaredispersedthroughoutthegenome ForExamples AlufamilyrRNAgenetRNAgeneHistonesgene Alufamilyinhuman Alufamilyisasetofdispersed relatedsequences each 300bplong inthehumangenome TheindividualmembershaveAlucleavagesites AGCT ateachend Thereare 300 000membersinthehaploidgenome equivalenttoonememberper6kbofDNA B1familyinMouse Arelatedsequencefamilyispresentinthemouse wherethe50 000membersarecalledtheB1family intheChinesehamster whereitiscalledtheAlu equivalentfamily andinothermammals 3 Highlyrepetitive HighlyrepetitiveDNAconsistsofveryshortsequencesthatarepresentmanytimesinthegenome oftenorganizedaslongtandemrepeats 串联重复 Neitherclassrepresentsprotein Becauseofitsshortrepeatingunit itissometimesdescribedassimplesequenceDNA 简单序列DNA Forexamples SatelliteDNAMinisatellites SatelliteDNA WheneukaryoticDNAiscentrifugedonadensitygradient twotypesofmaterialmaybedistinguished MostofthegenomeformsacontinuumoffragmentsthatappearasaratherbroadpeakcenteredonthebuoyantdensitycorrespondingtotheaverageG Ccontentofthegenome Thisiscalledthemainband Sometimesanadditional smallerpeak orpeaks isseenatadifferentvalue ThismaterialisthesatelliteDNA MouseDNAisseparatedintoamainbandandasatellitebycentrifugationthroughadensitygradientofCsCl 4 InvertedrepetitiveDNA1 SinglestrandToformastemloopstructure 2 Doublestrand palindromicsequence cruciformstructure 5 3EukaryoticGenes 1 WhattypeofDNAcorrespondstoprotein codinggenes ReassociationkineticstypicallyshowthatmostmRNAisderivedfromnonrepetitiveDNA Totalgenenumberisknownforseveralorganisms 20 ofDrosophilagenescodeforproteinsconcernedwithmaintainingorexpressinggenes 20 forenzymes 10 forproteinsconcernedwiththecellcycleorsignaltransduction HalfofthegenesofDrosophilacodeforproductsofunknownfunction housekeepinggenes 持家基因 Thecommonsetofexpressedgenefunctions comprisefunctionsthatareneededinallcelltypes Thesearecalledhousekeepingorconstitutive 组成性 genes numberingperhaps 10 000inamammal luxurygenesTheactivitiesrepresentedbyspecializedfunctions suchasovalbuminorglobin neededonlyforparticularcellphenotypes Thesearesometimescalledluxurygenes StructuralgenesStructuralgenecodesforanyRNAorproteinproductotherthanaregulator In1977 RichardJ RobertsandPhillipA SharpmadetheiramazingdiscoveryofsplitgenesintheadenoviruswhentheyexaminedahybridbetweenaviralmRNAanditstemplateDNAintheelectronmicroscope 2 Splitgene Thediscoveryofsplitgenes IntronisasegmentofDNAthatistranscribed butremovedfromwithinthetranscriptbysplicingtogetherthesequences exons oneithersideofit Intronsofnucleargenesgenerallyhaveterminationcodonsinallreadingframes andhavenocodingfunction ExonisanysegmentofaninterruptedgenethatisrepresentedinthematureRNAproduct RNAsplicingistheprocessofexcisingthesequencesinRNAthatcorrespondtointrons sothatthesequencescorrespondingtoexonsareconnectedintoacontinuousmRNA InterruptedgenesareexpressedviaaprecursorRNA Intronsareremovedwhentheexonsaresplicedtogether ThemRNAhasonlythesequencesoftheexons 对于割裂基因应注意的几点 Allclassesofgenesmaybeinterrupted nucleargenescodingforproteins nucleolargenescodingforrRNA andgenescodingfortRNA Interruptionsalsoarefoundinmitochondrialgenesinlowereukaryotes andinchloroplastgenes Interruptedgenesdonotappeartobeexcludedfromanyclassofeukaryotes andhavebeenfoundinbacteriaandbacteriophages althoughtheyareextremelyrareinprokaryoticgenomes Positionsofintronsareconservedwhentheorganizationofhomologousgenesiscomparedbetweenspecies 在不同生物的同源基因的组织中 内含子的位置是保守的 Intronsequencesvary andmayevenbeunrelated althoughexonsequencesremainwellrelated 内含子序列的变化关系不大 但外显子序列须保持不变 Variationsinthelengthsofthegenesareprimarilydeterminedbythelengthsoftheintrons i e Exonscodingforproteinsareusuallyshort 基因组基因的长度主要是由内含子的长度决定的 MammaliangenesforDHFR dihydrofolatereductase havethesamerelativeorganizationofrathershortexonsandverylongintrons butvaryextensivelyinthelengthsofcorrespondingintrons Intronsinvertebrategenesrangefromveryshorttoverylong Exonscodingforproteinsareusuallyshort Alltypesofeukaryoticgenomescontaininterruptedgenes 所有真核生物的基因组中均含有割裂基因 Theproportionofinterruptedgenesislowinyeastsandincreasesinthelowereukaryotes 割裂基因在酵母中所占比例少 而在较低等的真核生物中有所增加 fewgenesareuninterruptedinhighereukaryotes Nointron histonegeneinterferongene IFN Mostgenesareuninterruptedinyeast butmostgenesareinterruptedinfliesandmammals Yeastgenesaresmall butgenesinfliesandmammalshaveadisperseddistributionextendingtoverylargesizes 3 Genefamily Genefamilyconsistsofasetofgeneswhoseexonsarerelated thememberswerederivedbyduplicationandvariationfromsomeancestralgene 真核生物的基因组中有许多来源相同 结构相似 功能相关的基因 这样一组基因称为基因家族 类别 1 简单多基因家族 5SrRNA基因结构相同 基因与基因间由中度重复序列隔开 2 复杂多基因家族 如海胆 果蝇的组蛋白基因 各个成员并不都是相同 3 由发育阶段控制的多基因家族 人球蛋白基因家族亚基有相似结构 Genefamily Pseudogenesareinactivebutstablecomponentsofthegenomederivedbymutationofanancestralactivegene 作为基因组的组成成分 由有活性的祖先基因突变而来的无活性 沉默 基因 Thenumberofpseudogenescanbelarge Thesequenceofhumanchromosome22shows 679genesand134pseudogenes Nonalleliccopies Two ormore identicalgenespresentonthesamechromosomearedescribedasnonalleliccopies Tandemrepeatsgene 特点 1 各成员之间有高度的序列一致性甚至完全相同 2 拷贝数高 常有几十个甚至几百个 3 非转录的间隔区通常长短一致 Mostorganismscontainmultiplecopiesofthegenesforthehistoneproteinsthatareamajorcomponentofthechromosomes andtherearealmostalwaysmultiplecopiesofthegenesthatcodefortherRNAs H1 H2A H2B H3 H4五种组蛋白基因彼此靠近构成一个重复单位 许多重复单位串联在一起 构成组蛋白基因的Tandemrepeats 所有真核组蛋白基因缺乏Intron Histonegene rRNAgene5 8s 18s 28s 5srRNA 前三者组成一个主体rRNA 作为一个重复单位 各重复单位之间是非转录间隔区 5srRNA存在于被非转录间隔区分开的串联重复单位中 但不与大片段rDNA紧密相连 RibosomalRNAisthepredominantproductoftranscription constitutingsome80 90 ofthetotalmassofcellularRNAinbotheukaryotesandprokaryotes ThenumberofmajorrRNAgenesvariesfrom7inE coli 100 200inlowereukaryotes toseveralhundredinhighereukaryotes rRNA基因串联重复单位的长度 kb packingratio 堆积比 ThelengthoftheDNAasanextendedmoleculewouldvastlyexceedthedimensionsofthecompartmentthatcontainsit TheDNAmustbecompressedexceedinglytightlytofitintothespaceavailable SoincontrastwiththecustomarypictureofDNAasanextendeddoublehelix structuraldeformationofDNAtobendorfolditintoamorecompactformistheruleratherthanexception 5 4PackageofEukaryoticgenomes Thelengthofnucleicacidismuchgreaterthanthedimensionsofthesurroundingcompartment packingratio 100003010 Nucleosomeisthebasicstructuralsubunitofchromatin consistingof 200bpofDNAandanoctamerofhistoneproteins HistonesareconservedDNA bindingproteinsofeukaryotesthatformthenucleosome thebasicsubunitofchromatin Nonhistonesincludealltheproteinsofchromatinexceptthehistones 2 Firstlevelofpackaging Nucleosome ThenucleosomeconsistsofapproximatelyequalmassesofDNAandhistones includingH1 Thepredictedmassofthenucleosomeis262kDa Histonesofcalfthymus ThenucleosomemaybeacylinderwithDNAorganizedintotwoturnsaroundthesurface ThetwoturnsofDNAonthenucleosomelieclosetogether Theheightofthecylinderis6nm ofwhich4nmisoccupiedbythetwoturnsofDNA Twopointsseparatedby80bpinthefreedoublehelixmayactuallybecloseonthenucleosomesurface MicrococcalnucleasedigestschromatininnucleiintoamultimericseriesofDNAbands Micrococcalnucleasereducesthelengthofnucleosomemonomersindiscretesteps Microccocalnucleaseinitiallycleavesbetweennucleosomes Mononucleosomestypicallyhave 200bpDNA End trimmingreducesthelengthofDNAfirstto 165bp andthengeneratescoreparticleswith146bp Coreparticleisadigestionproductofthenucleosomethatretainsthehistoneoctamerandhas146bpofDNACoreDNAhasaninvariantlengthof146 145 bp andisrelativelyresistanttodigestionbynucleases LinkerDNAcomprisestherestoftherepeatingunit Itslengthvariesfrom8 114bp average 55bp pernucleosome Inasymmetricalmodelforthenucleosome theH32 H42tetramerprovidesakernelfortheshape OneH2A H2Bdimercanbeseeninthetopview theotherisunderneath Thecorehistonesformtwotypesofcomplexes H3andH4formatetramer H32 H42 VariouscomplexesareformedbyH2AandH2B inparticularadimer H2A H2B Invitro DNAcaneitherinteractdirectlywithanintact crosslinked histoneoctamerorcanassemblewiththeH32 H42tetramer afterwhichtwoH2A H2Bdimersareadded HistoneH1wasfoundoutsidethecorenucleosome nearthepointwhereDNAentersandexitsthecoreparticle The10nmfiberisacontinuousstringofnucleosomes The30nmfibermayhaveahelicalcoilof6nucleosomesperturn organizedradially 3 Secondlevelofpackaging 30nmfiber 4 Thirdlevelofpackaging radialloops Histone depletedchromosomesconsistofaproteinscaffoldtowhichloopsofDNAareanchored Scaffoldofachromosomeisaproteinstructureintheshapeofasisterchromatidpair