生物信息学4 陈润生PPT课件

,一、系统生物学的出现与发展,Forthepast30-40years,biologyatthemolecularandcellularlevelhasbeenstudiedfromtheperspectiveofanalyzingindividualgenesandindividualproteins.Systemsbiology,ontheotherhand,isinterestedinanalyzingwholesystemsofgenesorproteins.Whatthismeansisthatweusetoolsforcapturinginformationfrommanydifferentelementsoftheoverallsystem.Andwehavetobeabletointegratetheinformationthatsobtainedfromallthedifferentbiologicallevels-DNAinformation,RNAinformation,proteininformation,proteininteractioninformation,pathwaysandsoforth.Theultimateobjectiveistousethisinformationtowritemathematicalmodelsthatarecapableofpredictingsomethingaboutthestructureofthebiologicsystemunderevaluationaswellaspredictingsomethingaboutitsproperties,givenparticularkindsofstimuliorperturbations.,（一）、什么是系统生物学,BesideshavingbeenamongthefirstscientiststoadvocatetheHumanGenomeProject,Dr.LeroyHoodiscreditedforhavingplayedaleadroleininventingautomatedDNAsequencersinthemid-1980s.Moreover,hehasremainedoverthepast30yearsattheforefrontofeffortstoshapethetechnologyscientistsusetodaytoread,recordandanalyzethemassivevolumesofinformationrequiredtofathomthesecretsoflife.AfteradistinguishedcareerattheCaliforniaInstituteofTechnology,Dr.Hoodmovedin1992totheUniversityofWashington,wherehecreatedthecross-disciplinaryDepartmentofMolecularBiotechnology.Today,Dr.HoodservesisPresidentoftheInstituteforSystemsBiology,anon-profitorganization.,SupposeyoureflyingoverManhattanandyoudliketofindouthowManhattanworks.Youdhavetostartbycataloguingtheinfrastructure,thebuildings,theroadways,thecommunicationchannels,thecars,thebusroutesandalltherestofit.Youdalsohavetostudyhowpowerwasbroughtintothecityandhowitwasusedanddissipated.Andyoudhavetostudytrafficpatterns,workhabits,humaninteractionsandagreatmanyotherthingswedonthavetimetotalkabouthere.Thenyoudhavetotakeallthatdataandintegratethemtodevelopamodelcapableofpredictinghowthecityfunctions.Anditsexactlythesameforbiologicalsystems.Wehavetogatherinformationatdifferentlevelsandfullyintegrateittoreallyunderstandhowsystemswork.,GenomeshighlighttheFinitenessofthe“Parts”inBiology,Bacteria,1.6Mb,1600genesScience269:496,Eukaryote,13Mb,6KgenesNature387:1,1995,1997,1998,Animal,100Mb,20KgenesScience282:1945,Human,3Gb,100Kgenes?,2000?,realthing,Apr00,98spoof,大规模基因功能表达谱的分析随着人类基因组测序逐渐接近完成，人们自然会提出如下的问题：即使我们已经获得了人的完整基因图谱，那我们对人的生命活动能说明到什么程度呢？人们进一步提出了一系列由上述数据所不能说明的问题，例如：基因表达的产物是否出现与何时出现；基因表达产物的定量程度是多少；是否存在翻译后的修饰过程，若存在是如何修饰的；基因敲除（knock-out）或基因过度表达的影响是什么；多基因差异表达与表现型关系如何等等。概括这些问题，其实质应该是：知道了核酸序列和基因，我们依然不知道它们是如何发挥功能的，或者说它们是如何按照特定的时间、空间进行基因表达的，表达量有多少。,.,microarrays,AffymetrixOligosDonthavetoknowsequenceGlassslidesPatbrown,.,功能图谱,FromCell,2001,V0l.104,333,基因组（Genome）转录组（Transcriptome）蛋白质组（Proteome）相互作用组（Interactome)定位组（Localizome）折叠子组（foldome）代谢组（Metabolome）表型组（Phenome）,后基因组研究对象的多层次,遗传图谱（Geneticmap）限制性图谱（Restrictionmap）物理图谱（Physicalmap）功能图谱（Functionalmaps）,“快照”,.,后基因组时代对功能理解的本质变化,S,P,A,序列,结构,功能,A,B,C,X,Y,V,Z,相互作用,网络,功能,.,研究思路的变化,FromCell,2001,V0l.104,333,更好整合生物过程不同阶段的分散数据.基因组+转录组+蛋白质组+代谢组满足复杂查询的整合数据库.对复杂生物过程的更好模拟.蛋白质折叠.复杂系统建模.Signaling/Metabolicpathways.Pathogenesis.生物过程动态研究.Fromthecomponentsofapathwaytothedynamicsofapathway.,功能基因组发展趋势,.,（二）、系统生物学研究的一些例子,.,基因通过复杂的多反馈网络发挥作用,复杂系统：一个病毒的基因和启动子相互作用的网决定了它是休眠还是复制,TRENDSINGENETICS5(2),67(1999),.,基因调控的网络模型,Science15Jan1999,Vol283,.,哺乳动物细胞周期调控网络(部分)。,Mol.Biol.Cell10,27032734(1999).,.,AnnotatingtheYeastGenome,NetworkofyeastSup35protein,NetworkofyeastSIRprotein,多信息融合的蛋白质功能注释（4NOV1999Vol402,Nature),.,半乳糖代谢通路研究（4May2001Vol292,Science),基于已有知识的基本模型,.,整合转录组和蛋白质组实验数据后获得的精细功能图谱,诺贝尔奖得主AlGilman主持,小鼠心肌细胞的钙信号通路,,.,E-cell,剥离的细胞由E-cell进行生物化学模拟,ScienceApril2,1999,Vol284,.,系统生物学（SystemsBiology）成为近年重要研究方向,TreyIdeker,etal,IntegratedGenomicandProteomicAnalysesofaSystemticallyPerturbedMetabolicNetwork,4May2001Vol292Science,MichaelTLaub,etal,GlobalAnalysisoftheGeneticNetworkControllingaBacterialCellCycle,15December,2000Vol290,Science,H.Jeong,etal.Lethalityandcentralityinproteinnetworks,Nature,Vol411,3MAY2001,GeorgevonDassow,EliMeir,Thesegmentpolaritynetworkisarobustdevelopmentalmodule,Nature,Vol406,13JULY2000,H.Jeong,etal,Thelarge-scaleorganizationofmetabolicsnetworks,Nature,v407,2000,ThomasSimonShimizu,etal,MolecularmodelofalatticeofsignallingproteinsinVolvedinbacterialchemotaxis,NatureCellBiology,Vol2,2000,MichaelB.Elowitz,etal,Asyntheticoscillatorynetworkoftranscriptionalregulators,Nature,v403,2000,S.Kalir,etal,OrderingGenesinaFlagellaPathwaybyAnalysisofExpressionKineticsfromLivingBacteria,Science,v292,2001,MatthewFreeman,Feedbackcontrolofintercellularsignallingindevelopment,Nature,v408,ChunyanXu,etal,OverlappingActivatorsandRepressorsDelimitTranscriptionalResponsetoReceptorTyrosineKinaseSignalsintheDrosophilaEye,Cell,Vol.103,2000,ThomasSurrey,FrancoisNedelec,PhysicalPropertiesDeterminingSelf-OrganizationofMotorsandMicrotubules,ScienceVol29211May2001,NorbertFrey,etal,DecodingcalciumsignalsinVolvedincardiacgrowthandfunction,NatureMedicine*Volume6*Number11*November2000,RekaAlbert,etal,Errorandattacktoleranceofcomplexnetworks,Nature,v406,2000,Nature415,123-124(2002),.,Nature415,141-147(2002),ModelingtheHeart-fromGenestoCellstotheWholeOrganSciencesVol2951March2002,MolecularNetworks:TheTop-DownViewDennisBrayScience26Sep2003,Theexhilaratingprogressofthepastdecadehasbroughtanunprecedentedwealthofquantitativeinformationonlivingsystems,fromgenomicsequencestoproteinstructuresandbeyond.Butalthoughtechnicaladvancesmakedatacollectionevereasier,investigatorsareincreasinglyconcernedbytheirinabilitytogainabiggerpicture.Howcanthisgrowingmountainoffactsbeassimilated,andwherewillthenewideascomefromthatwillhelpusgainabroaderperspective?Networks,.,（三）、系统生物学的研究思路,.,多信息融合构建功能图谱,FromCell,2001,V0l.104,333,.,FromCell,2001,V0l.104,333,系统生物学研究方法的创新点,生物复杂系统的突现性规律，如钙波功能基因组多层次系统的贯穿特性系统与系统，层次与层次的相互作用新方法支持向量机主成分分析（时频分析、偏最小二乘等）功能子系统建模多信息融合,.,EmergentPropertiesofNetworksofBiologicalSignalingPathwaysScience15Jan1999,VOL283,.,.,酵母细胞周期表达谱分析共调控基因,Nature,2000,Vol405,15,.,大规模基因表达谱用于基因调控网络构建,.,（四）、可能的应用,.,肿瘤研究,.,肿瘤研究,.,心血管疾病研究,.,SpectralAnalysisoftheProtein-proteinInteractionNetworkinBuddingyeast,.,Thetopologicalstructureinprotein-proteininteractionnetworkInclique,proteinsconnectquitetightly,almostinteractingwitheachother.However,ineachbipartite,proteinsweredividedintotwoparts,proteinsseldomconnectinsamepartsbutconnecttightlywithproteinsincounterpart.,AClique,bBipartite,Thepercentageoffunctionclassesineveryclique,FunctionpredictionforSSUprocessome,Theprotein-proteininteractionnetwork:beforeandafterspectralanalysis,.,二、非编码区功能研究,BREAKTHROUGHOFTHEYEAR(2001):Sciencecelebratesnineotherareasinwhichimportantfindingswerereportedthisyear,fromsubatomictoatmosphericandbeyond.Firstrunner-up:RNAascending.,ShortRNAsclearlyplayimportantbiologicalroles.Dozensofthemoleculesarenowknowntoexistinthenematodeandfruitfly.ThecodingforthesemoleculesiscontainedintheDNAsequence.Some100ofthesetinyRNAgeneshavebeenfoundinthegutbacteriumEscherichiacoli,andsome200wereuncoveredinDNAfrommousebraintissue.Inthenematodeandfruitfly,theyseemtobeinvolvedindevelopment;inE.coli,theymayfacilitaterapidresponsestoenvironmentalchangeandcouldservesimilarfunctionsinmammals.,Whatisagenome?,1911-gene:Elementaryunit,responsibleforthetransmissionofhereditarycharacters1920-genome:Setofgenesofanorganism1944-Averyetal.DNAisthemoleculeofheredity1950-70:Doublehelix,GeneticcodeGenome=setofDNAmoleculespresentinacellandtransmittedtotheoffspring,Agenomeismorethanasetofgenes,Genes(transcriptionunit):Protein-codinggenesRNAgenes:rRNAs,tRNAs,snRNAs,etc.UntranslatedRNAgenes(e.g.Xist,H19)Regulatoryelements(promoters,enhancers,etc.)Elementsrequiredforchromosomereplication(replicationorigins,telomeres,centromeres,etc.)Non-functionalsequencesNon-codingsequencesRepeatedsequencesPseudogenes,Genomesize,Numberofproteingenes,HumanvsE.coli:Genomesize:x1000Numberofgenes:x10,Proportionoffunctionalelementswithingenomes,Functionalelementsinthehumangenome,non-translatedRNAgenes:Xist,H19,His-1,bic,microRNAs,etc.Regulatoryelements:promoters,enhancers,etc.Transposableelements(LINEs,SINEs,.):40-45%,86%no(known)function,intergenicDNA60-70%,Introns25%,Codingregions(proteins)1.7%,tRNA,rRNA,0,5%,SatelliteDNA(centromeres,telomeres)12%,3.4109nt30000-40000proteingenes,Repeatedsequences,TandemrepeatsSatelliteMinisatelliteMicrosatelliteInterspersedrepeatsDNAtransposonsRetroelements,Tandemrepeats,motifblocsize%humangenomesatellite:2-2000ntupto10Mb10%minisatellite:2-64nt100-20,000bp?microsatellite:1-6nt10-100bp2%SlippageoftheDNApolymerase:CACACACACACAUnequalcrossing-over:,Centromeres,telomeres:SatelliteDNA,Interspersedrepeats,Transposableelements(autonomousornon-autonomous):DNAtransposons(rareinmammals)Retroelements,Retroelements,LINEs(longinterspersedelements):6-8kbretroposonsSINEs(shortinterspersedelements):80-300bpsmall-RNA-derivedretrosequences(tRNA),polIIIEndogenousRetroviruses:1.5-10kb,Frequencyoftransposableelementsinthehumangenome,Total=42%(Smit1999)Probablyunderestimated,Thefrequencyoftransposableelementsisnotuniformalongthehumangenome:er-chromosomicvariations(Smit1999),Pseudogenes,Afterageneduplication:evolutionofnewfunction(sub-functionalizationorneo-functionalization)orgeneinactivation,Retropseudogenes,Retropseudogenes,23,000to33,000retropseudogenesinthehumangenomeOftenderivefromhousekeepinggenes,非编码区功能研究是最挑战性的课题Whatisthetotalnumberofhumangenes?28,0004,000Only1.1%ofthegenomeisspannedbyexons,whereas24%isinintrons,with75%ofthegenomebeingintergenicDNA.Oneofthelargestchallengesisidentifyingtheunknownfunctionsthatalmostcertainlyexistinmuchofthe“junk”DNA.,OrganismYearMillionsTotalPredictedNumberofgenesofbasescoveragenumberpermillionbasessequenced(%)ofgenessequencedHumangenomeroughdraft20012,6938431,78012(publicsequence)Humangenomeroughdraft20012,6548339,11415(Celerasequence)Humanchromosome21200034752257Humanchromosome221999347054516Arabidopsisthaliana20001159225,498221Drosophilametanogaster20001166413,601117Caenorhabditiselegans1998979919,099197Saccharomycescerevisiae199612935,800483,CodingDNA:11.5%NoncodingDNA:intron24%intergenicDNA75%promotertelomeresrepetitive45%LINE21850,000（拷贝数）SINE131,500,000LTR8450,000Transposons3%300,000Noncodingandnonrepetitive35%LINEplayacrucialroleinXinactivation,theprocessbywhichoneofthetwoXchromosomesinafemaleisturnedoffearlyindevelopment.SmallRNA,重复序列在基因组中的比例Human45%Arabidopsis11%C.elegans7%D.melanogaster3%,Mammaliangenomes:summary,Genes,regulatoryelements:2%Non-codingsequences:98%SatelliteDNA(centromeres)10%Microsatellites2%Transposableelements42%Pseudogenes1%Other(ancienttransposableelements?)43%Variationsingeneandrepeatdensityalongchromosomes,Genenumbersdonotincreaseasmuchasexpectedwithcomplexity:-wormandflygenenumbers(12-14,000)areonlyabouttwicethoseofyeast(6,000)andP.aeruginosa(5,500)-mammalian(human,mouse)genenumbers(30,000)areonlyabouttwicethoseofinvertebrates.,Thecomplexityproblem,Thissuggeststhat:-animalshavearelativelystablecoreproteome,whosecomponentsaremultitaskedindifferentiationanddevelopment-variationsinphenotypeoccursmainlybyvariationinthecontrolarchitecture(unlikeprokaryotes),Phenotypicvariationinmammalsisprimarilyassociatedwithnoncodingregions:-only10,000outof3,000,000polymorphismsbetweenindividualhumans(0.3%)occurinproteincodingsequences-only1%ofgenesaredifferentbetweenhumansandmice.,98%oftranscriptionaloutputinhumansisnoncodingRNA,ExcisedintronsandothernoncodingRNAsappeartoberelativelystable(notdegradedrapidlyasisusuallythought),Someintrons/noncodingRNAsarehighlyconserved,e.g.:-Drosophilaadhgeneintron1,trageneintron2,let-7-Mouse/humanT-cellreceptorgene-Human/Xenopusg-actinintron3-butmostnotsequenced.,EvidenceforRNA-mediatedgeneregulation-lin4/lin14andlet7/lin41inC.elegans-smallnucleolarRNAs-H19,XIST,roX1/roX2-Drosophilabithorax-abdominalA/BlocusofDrosophila-200kb,7majortranscripts-only3codeforprotein,all7aredevelopmentallyregulatedandallhavegeneticsignatures,一、NoncodingRNA功能的例子,SINEelementsserveasrecombinationhot-spotsallowingtheexchangeofgeneticmaterialbetweenunrelatedsequences.SINEsastranslatedpartsofhostgenes,SINEsasasourceofregulatoryelements,Theinsertionofarepetitivesequenceintoagenecaninfluenceitstranscription.TheSINEsandotherrepeatscanactastissue-specificenhancersorsilencersoftheadjacentgenes.Steineretal.showedthatinthechickenlysozymegene,aCR1elementlocatedupstreamofthecodingregionactsasatranscriptionalsilencer.SafferandThurstonshowedthatanegativeregulatoryelementofthe7.02bidirectionalpromoterintheAfricangreenmonkeyispartofanAlusequence.ThehumanCD8ageneisregulatedinT-cellsbyanenhancerlocatedinthelastintron.The5partoftheenhancerconsistsofafullAluelementinsertedinthesenseorientation.AnL1elementlocatedabout3kbupstreamoftheratinsulin-1geneactsasasilencer,X-inactivationisthemammaliandosagecompensationmechanism,usedtoequalizeX-linkedgenedosagebetweenmaleandfemalecells.InmammalsdosagecompensationoccursbythetranscriptionalsilencingofoneXchromosomeinallfemalesomaticcells.ThesilencingoftheinactiveXchromosomeisachievedbyanXchromosomewidealterationinchromatinstructure,fromactiveeuchromatintoinactiveheterochromatin.X-inactivationisnucleatedandbidirectionallypropagatedfromtheX-inactivationcenter.TheXistgenelieswithintheX-inactivationcenterandisrequiredtoinitiateXchromosomeinactivation.Xistencodesalarge,spliced,polyadenylated,noncodingRNAthatisexpressedexclusivelyfromtheotherwiseinactiveXchromosome.CytologicallyXistRNAappearsasaclusterofparticlesthatcoattheinactiveXchromosome.SpreadofXistRNAcorrelatestemporallywiththespreadofsilencingalongtheXchromosome.ThetwomostinterestingquestionsthatarisefromthischaracterizationofXistare:howdoesXistRNAfunctioninalteringchromatinstructureandhowisXistitselfregulated?/pibs/faculty/panning.htmlBarbaraPanningLab,SmallRNAandRNAInterference(RNAi）,AnumberofrecentreportshaveshownthatsmallRNAmoleculesplaysignificantrolesinbothgenesilencingandregulationofdevelopmentaltiming.Small,processeddouble-strandedRNAs(alsocalledshortinterferingRNAsorsiRNAs)mediatethephenomenonknownasRNAinterference(RNAi)post-transcriptionalgenesilencing(PTGS)inducedbytheintroductionofdsRNAandhavebiologicalrolesinviralresistanceinplantsandtransposonsilencinginCaenorhabditiselegans.AnothergroupofsmallRNAmolecules,knownassmalltemporalRNAs(stRNAs),regulatesC.elegansdevelopmentaltimingthroughtranslationalrepressionoftargettranscripts.InRNAi,dsRNAintroducedintosusceptibleorganismsisprocessedinto22nucleotide(nt)siRNAs.These22ntsiRNAssubsequentlybindtothehomologousregionoftheirtargettranscriptandtagitfornucleasecleavage.ThusgenesilencingiseffectedbydestructionofthetargetmRNA.,Timeline,Late70slin-4andlet-7regulatedevelopmentaltiminginworm1993lin-4codesfora22ntRNA,complementaryto3UTRoflin-142000.sodoeslet-7(stRNAs)2000let-7isconservedinbilaterallysymmetricanimals2001100miRNAsdiscoveredbycloninginworm,flyandhuman2002miRNAsconservedinplants2002Sciencemagazinesbreakthroughoftheyear2002miRNARegistryestablished2003miRNAsmayaccountfor1%oftotalgenecountinanimals2003afewtargetsofmiRNAsidentified2004miRNARegistryhas719miRNAs,长期以来人们一直认为RNA分子的主要作用是与蛋白质合成有关，无论是tRNA,rRNA还是mRNA，它们一起构成一套精密的机构将DNA中的基因信息传递到蛋白质。但自上世纪九十年代以来对小片段RNA研究的一系列新发现，使人们不得不重新认识RNA在生命活动中的重要作用。其中最突出的例子是由研究基因沉默现象（GeneSilencing）而导致RNA干涉（RNAInterference，RNAi）的发现。转录后基因沉默（Post-transcriptionalgenesilencing，PTGS）,最早发现存在于矮牵牛和少数几种植物当中。这种特殊现象表现为，当对这些植物进行转基因后，导入的基因和其相似的内源基因同时都被抑制。进一步的实验表明同源转录本确实出现过，但是很快被降解了。对这一现象的深入研究开始于上世纪的九十年代。当时一些科学家以线虫（Caenorhabditiselegans）为对象探讨用反义RNA去阻断基因的表达，结果反义RNA的确能够阻断基因的表达，但是奇怪的是，作为对照的正义链RNA也同样阻断了基因的表达。此后另一些科学家以同时包含正义链和反义链的双链RNA（double-strandedRNA，dsRNA）去阻断基因的表达，结果表现出比单独注射正义链或者反义链都要强得多的基因沉默现象。这种由RNA导致的基因沉默现象被称为RNA干涉（RNAinterference,简称RNAi）。,对RNA干涉机制的研究发现：dsRNA一旦进入细胞内，就会被一个称为Dicer的特定的酶切割成为21-23核苷酸长的小分子干扰RNA（smallinterferingRNAs，siRNA）片段，Dicer酶属于RNaseIII家族中能特异识别双链RNA的成员，它以ATP依赖的方式切割由外源导入或者由转基因、病毒感染等各种方式引入的双链RNA。切割产生的siRNA片段随后与一些酶结合成为诱导沉默复合体（RNA-inducedsilencingcomplex，RISC）。激活的RISC通过碱基配对定位到与siRNA同源的mRNA转录本上，并在距离siRNA3端一定的位置上切割该mRNA。这样就使与此mRNA相应的特定基因成为沉默状态。继线虫之后，在果蝇中也发现了RNA干涉。现大量研究已表明，RNA干涉广泛存在于从真菌到植物、从无脊椎动物到晡乳动物的各种生物中，甚至也存在于低等的原核生物中。从遗传学、分子生物学和生化学角度进行的研究也指出转录后基因沉默（PTGS）和RNA干涉可能在生命进化的早期就存在。有人提出转录后基因沉默可能是进化过程中一种抵御转座子或RNA病毒的防御机制，是生物使用的一种古老的抗病毒策略，可能在植物和动物分化之前就已经出现。,miRNAbiogenesis,AdaptedfromDPBartel,Cell116:281-297(2004),上世纪九十年代美国Dartmouth医学院VictorAmbros小组的研究结果表明，其实这样的RNA就存在于生物体自身。他们以线虫为对象用基因打靶技术研究某些基因对其发育的影响。他们找到了一个对发育有明显干扰的基因。通常线虫要通过四个幼虫阶段才能成熟，这个基因的突变使其只停留在第一阶段。令人们惊奇的是这个基因并不编码任何蛋白质，而是编码一个小RNA。以后的研究证明，这样的小RNA基因在果蝇、软体动物、鱼类以及人体中都存在。有研究报道在大肠杆菌中已经发现几十个小RNA的基因，在小鼠的脑组织中发现了200多个小RNA基因。现在科学家们正系统地在各种生物中寻找小RNA基因。,小RNA和RNA干涉研究具有广泛的应用前景，有的科学家认为它有可能掀起一场生物革命。首先RNAi是一项快速、高效、便于操作的使靶基因失活的技术。因此它可以象基因敲除一样非常有效地鉴定特定基因的功能。随着各种模式生物体的基因组计划的完成，生物学家们已经可以方便的从数据库中获得全基因组序列，从而找到研究者感性趣基因的序列，据此设计出dsRNA就可以使该基因沉默。这是研究疾病机理和鉴定候选药靶的关键步骤，也为将来可控地打开或者关闭某一特定基因这一目标奠定了基础。现已有两个研究组使用了RNAi技术分别对两条线虫染色体上的全部基因进行大规模的功能研究，并正在利用该技术对线虫全基因组进行研究。RNA干涉也为疾病的治疗开辟了新的途径。RNA干涉理论上能减少肝炎病毒感染所需的蛋白质，而达到减少病毒数量的目的；也可以用来减少某些遗传疾病的不正常基因的蛋白质制造量，以治疗该疾病。例如，多谷胺酸聚合疾病，包括脊髓小脑运动失调症和亨庭顿氏症。甚至可以通过抑制病毒或HIV自身的信使RNA来抵抗病毒感染尤其是HIV感染。,治疗SARS的RNAi设计NumbersofeligiblesiRNAcandidatetargetsselectedbasedontheoreticaldesign,1)Correspondingproteins:proteinscodedbythegenewheretargetsequencesposition.,SequencesofseveralrepresentativesiRNAcandidatetargets,1)Correspondingproteins:proteinscodedbythegenewheretargetsequencesposition;2)Positionof5end:the5endpositionofsiRNAcandidatetargetssequencerelativetoSARS-CoVgenome.,2002年小RNA研究又取得了新的进展。几组科学家研究了酵母和四膜虫这两种生物体中的RNA干扰现象，他们发现小RNA对染色质的形状有着极大的控制作用。即，小RNA能够永久性关闭或删除一部分DNA（其机制现在还不了解），而不只是简单地使DNA暂时沉默。冷泉港实验室的ShivGrewal、RobertMartienssen等发现缺失平常的小RNA的裂殖酵母细胞不能在中心粒正确形成异染色质，从而破坏了正常的细胞分裂。弗吉尼亚大学的DavidAllis等和罗切斯特大学的MartinGorovsky等也发现，小RNA能引发四膜虫（Tetrahymena）细胞分裂期间的DNA缺失或序列重组。这些新发现只是小RNA研究领域的一小部分，科学家们正试图确定成百种小RNA各自的功能；确定哪些物种含有哪类小RNA以及它们在该物种中的行为是什么？小RNA的出现重新唤起了科学家们对“RNA世界”的重视及对“生命起源于RNA分子”这一命题的兴趣。有的科学家认为成千上万非编码蛋白质的RNA分子组成了巨大的分子网络调节着细胞中的生命活动，它们与蛋白质-蛋白质相互作用网络相对应，好比宇宙学中的暗物质，将为基因组和生命科学研究提供无比美好的前景。,miRNAstargets,DPBartel,Cell2004116:281-287,C.elegans,A.thaliana,Structuraldifferences,ad