基因组与染色体

Chapter5Genomeandchromosome§5-1Genomesize§5-2Eukaryoticgenomes§5-3Eukaryoticgenes§5-4PackageofEukaryoticgenomes§5-5Prokaryoticgenomesandpackage§5-6GenomeCharacteristicsofAnimalVirusChromatin:

describestheconditionofthechromosomalmaterialduringtheinterphase(betweenmitoses)ofthecellcycle.

Chromosome:

isadiscreteunitofthegenomecarryingmanygenes.EachchromosomeconsistsofaverylongmoleculeofduplexDNAandanapproximatelyequalmassofproteins.Itisvisibleasamorphologicalentityonlyduringcelldivision.

Nucleoid:

isthecompactbodythatcontainsthegenomeinabacterium.§

5-1GenomesizeandchromosomeKeyterms:TranscriptomeisthecompletesetofmRNAspresentinacell,tissue,ororganism.(?!)Proteomeisthetotalnumberofproteinsproducedbyanorganism.

Genomeisthecompletesetofsequencesinthegeneticmaterialofanorganism.ItincludesthesequenceofeachchromosomeplusanyDNAinorganelles.1.C-valueThetotalamountofDNAinthehaploidgenomeisacharacteristicofeachlivingspeciesknownasitsC-value.

ThereisenormousvariationintherangeofC-values,from<106bpforamycoplasmato>1011bpforsomeplantsandamphibians.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-value

isrelatedtothemorphologicalcomplexityoflowereukaryotes,butvariesextensivelyamongthehighereukaryotes.Thegenomesizesofsomecommonexperimentalorganisms藻类粘菌线虫Conclusions:▲Wecanseethesteadyincreaseingenomesizewithmorphologicalcomplexityinsomeofthemostcommonlyanalyzedorganisms.▲▲Asweclimbtheevolutionarytree,however,therelationshipbetweenmorphologicalcomplexityoftheorganismandcontentofDNAesobscure.▲▲▲Buttherearesomeextremelycuriousvariationsinrelativegenomesize.ForExample:☆ThetoadXenopus(蟾蜍)andmanhavegenomesofessentiallythesamesize.☆☆

AndinsomephylathereareextremelylargevariationsinDNAcontentbetweenorganismsthatdonotvarymuchinmorphological

complexitysuchasamphibians,andplants.☆☆☆Inamphibians,thesmallestgenomesare<109bp,whilethelargestare~1011bp.Thereisunlikelytobealargedifferenceinthenumberofgenesneededtospecifytheseamphibians.Why?2.C-valueparadoxItreferstothelackofacorrelationbetweengenomesizeandgeneticcomplexity.

ThereisanexcessofDNAcomparedwiththeamountthatcouldbeexpectedtocodeforprotein.

TherearelargevariationsinC-valuesbetweencertainspecieswhoseapparentcomplexitydoesnotvarymuch.Twopuzzlingfeatures:Thesequestionscanbedirectlyansweredbygenomesequences,butatpresentwehavedirectinformationforonlyafewindividualgenomes.§5-2EukaryoticgenomesSeveralsequencecomponentsineukaryoticgenomes:NonrepetitiveDNAconsistsofsequencesthatareunique:thereisonlyonecopyinahaploidgenome.RepetitiveDNAdescribessequencesthatarepresentinmorethanonecopyineachgenome.RepetitiveDNAisoftenclassedintotwogeneraltypes：

Moderatelyrepetitive:10~几百个

Highlyrepetitive：几百~几百万个InvertedrepetitiveDNAThelengthofthenonrepetitiveDNAcomponenttendstoincreasewithoverallgenomesize.(sometimesthoseof2~3copiesarealsocallednonrepetitiveDNA)ThenonrepetitiveDNAcontentofgenomesthereforeaccordsbetterwithoursenseoftherelativecomplexityoftheorganism.Forexample:E.coli4.2×106bpC.elegans6.6×107bpD.melanogaster~108bpmammals~2×109bp.

Furtherincreaseingenomesize,however,generallyreflectsanincreaseintheamountandproportionoftherepetitivecomponents.1.NonrepetitiveDNATheproportionsofdifferentsequencecomponentsvaryineukaryoticgenomes.TheabsolutecontentofnonrepetitiveDNAincreaseswithgenomesize,butreachesaplateauat~2109bp.2.ModeratelyrepetitiveModeratelyrepetitiveDNAconsistsofrelativelyshortsequencesthatarerepeatedtypically300-1000bpinthegenome.Thesequencesaredispersedthroughoutthegenome.ForExamples:

AlufamilyrRNAgenetRNAgeneHistonesgeneAlufamilyinhuman:

Alufamilyisasetofdispersed,relatedsequences,each~300bplong,inthehumangenome.TheindividualmembershaveAlucleavagesites(AGCT)ateachend.Thereare~300,000membersinthehaploidgenome(equivalenttoonememberper6kbofDNA).B1familyinMouse:

Arelatedsequencefamilyispresentinthemouse(wherethe50,000membersarecalledtheB1family),intheChinesehamster(whereitiscalledtheAlu-equivalentfamily),andinothermammals.3.HighlyrepetitiveHighlyrepetitiveDNAconsistsofveryshortsequencesthatarepresentmanytimesinthegenome,oftenorganizedaslongtandemrepeats（串联重复）.Neitherclassrepresentsprotein.Becauseofitsshortrepeatingunit,itissometimesdescribedassimplesequenceDNA（简单序列DNA）.Forexamples:

SatelliteDNA

MinisatellitesSatelliteDNA:WheneukaryoticDNAiscentrifugedonadensitygradient,twotypesofmaterialmaybedistinguished:MostofthegenomeformsacontinuumoffragmentsthatappearasaratherbroadpeakcenteredonthebuoyantdensitycorrespondingtotheaverageG/Ccontentofthegenome.Thisiscalledthemainband.Sometimesanadditional,smallerpeak(orpeaks)isseenatadifferentvalue.ThismaterialisthesatelliteDNA.MouseDNAisseparatedintoamainbandandasatellitebycentrifugationthroughadensitygradientofCsCl.4.InvertedrepetitiveDNA

1）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.StructuralgenesStructural

genecodesforanyRNAorproteinproductotherthanaregulator.？？！！In1977,RichardJ.RobertsandPhillipA.SharpmadetheiramazingdiscoveryofsplitgenesintheadenoviruswhentheyexaminedahybridbetweenaviralmRNAanditstemplateDNAintheelectronmicroscope.2.SplitgeneThediscoveryofsplitgenesIntronisasegmentofDNAthatistranscribed,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)havethesamerelativeorganizationofrathershortexons(totallylessthan1.0kb)andverylongintrons,butvaryextensivelyinthelengthsofcorrespondingintrons.Intronsinvertebrategenesrangefromveryshorttoverylong.ExonscodingforproteinsareusuallyshortAlltypesofeukaryoticgenomescontaininterruptedgenes.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.

Nointrons:histonegeneinterferongene(IFN)Mostgenesareuninterruptedinyeast,butmostgenesareinterruptedinfliesandmammals.Yeastgenesaresmall,butgenesinfliesandmammalshaveadisperseddistributionextendingtoverylargesizes.3.GenefamilyGenefamilyconsistsofasetofgeneswhoseexonsarerelated;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(中度重复)。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（基因家族）。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。HistonegenerRNAgene5.8s,18s,28s,5srRNA,前三者组成一个主体rRNA基因，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）物种重复单位长间隔区长转录区长啤酒酵母8.951.757.2黑腹果蝇11.5-14.23.75-6.457.75非洲爪蟾10.5-13.52.3-5.37.875小鼠443018.4packingratio（堆积比）

ThelengthoftheDNAasanextendedmoleculewouldvastlyexceedthedimensionsofthecompartmentthatcontainsit.TheDNAmustbecompressedexceedinglytightlytofitintothespaceavailable.SoincontrastwiththecustomarypictureofDNAasanextendeddoublehelix,structuraldeformationofDNAtobendorfolditintoamorecompact

formistheruleratherthanexception.§5-4PackageofEukaryoticgenomes

Thelengthofnucleicacidismuchgreaterthanthedimensionsofthesurroundingcompartment.packingratio

>10000

30

10Nucleosomeisthebasicstructuralsubunitofchromatin,consistingof~200bpofDNAandanoctamerofhistoneproteins.HistonesareconservedDNA-bindingproteinsofeukaryotesthatformthenucleosome,thebasicsubunitofchromatin.Nonhistonesincludealltheproteinsofchromatinexceptthehistones.

2.Firstlevelofpackaging-

Nucleosome

ThenucleosomeconsistsofapproximatelyequalmassesofDNAandhistones(includingH1).Thepredictedmassofthenucleosomeis262kDa.HistoneAminoacidsLysArgMWH121529%1%23000H2A12911%9%14500H2B12516%6%13774H313510%13%15324H410211%14%11282HistonesofcalfthymusThenucleosomemaybeacylinderwithDNAorganizedintotwoturnsaroundthesurface.ThetwoturnsofDNAonthenucleosomelieclosetogether.Theheightofthecylinderis6nm,ofwhich4nmisoccupiedbythetwoturnsofDNA.Twopointsseparatedby80bpinthefreedoublehelixmayactuallybecloseonthenucleosomesurface.MicrococcalnucleasedigestschromatininnucleiintoamultimericseriesofDNAbandsMicrococcalnucleasereducesthelengthofnucleosomemonomersindiscretesteps.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.ABA：H1缺失是的核小体结构；B：H1存在时核小体的结构The10nmfiberisacontinuousstringofnucleosomes.

The30nmfibermayhaveahelicalcoilof6nucleosomesperturn,organizedradially.3.Secondlevelofpackaging-30nmfiber4.Thirdlevelofpackaging-radialloopsHistone-depletedchromosomesconsistofaproteinscaffoldtowhichloopsofDNAareanchored.

Scaffoldofachromosomeisaproteinstructureintheshapeofasisterchromatidpair,generatedwhenchromosomesaredepletedofhistones.Nuclearmatrix:afilamentousstructureontheinteriorofthenuclearmembraneininterphasecells.MAR(matrixattachmentsite;alsoknownasSARforscaffoldattachmentsite)isaregionofDNAthatattachestotheproteinstructuresininterphasenuclei.

Bacterialstructuralgenesareoftenorganizedintoclustersthatincludegenescodingforproteinswhosefunctionsarerelated.Itiscommonforthegenesfortheenzymes