一、系統生物學出現與發展1/161Forthepast30-40years,biologyatthemolecularandcellularlevelhasbeenstudiedfromtheperspectiveofanalyzingindividualgenesandindividualproteins.Systemsbiology,ontheotherhand,isinterestedinanalyzingwholesystemsofgenesorproteins.Whatthismeansisthatweusetoolsforcapturinginformationfrommanydifferentelementsoftheoverallsystem.Andwehavetobeabletointegratetheinformationthat'sobtainedfromallthedifferentbiologicallevels--DNAinformation,RNAinformation,proteininformation,proteininteractioninformation,pathwaysandsoforth.Theultimateobjectiveistousethisinformationtowritemathematicalmodelsthatarecapableofpredictingsomethingaboutthestructureofthebiologicsystemunderevaluationaswellaspredictingsomethingaboutitsproperties,givenparticularkindsofstimuliorperturbations.（一）、什么是系統生物學2/161BesideshavingbeenamongthefirstscientiststoadvocatetheHumanGenomeProject,Dr.LeroyHoodiscreditedforhavingplayedaleadroleininventingautomatedDNAsequencersinthemid-1980s.Moreover,hehasremainedoverthepast30yearsattheforefrontofeffortstoshapethetechnologyscientistsusetodaytoread,recordandanalyzethemassivevolumesofinformationrequiredtofathomthesecretsoflife.AfteradistinguishedcareerattheCaliforniaInstituteofTechnology,Dr.Hoodmovedin1992totheUniversityofWashington,wherehecreatedthecross-disciplinaryDepartmentofMolecularBiotechnology.Today,Dr.HoodservesisPresidentoftheInstituteforSystemsBiology,anon-profitorganization.

3/161Supposeyou'reflyingoverManhattanandyou'dliketofindouthowManhattanworks.You'dhavetostartbycataloguingtheinfrastructure,thebuildings,theroadways,thecommunicationchannels,thecars,thebusroutesandalltherestofit.You'dalsohavetostudyhowpowerwasbroughtintothecityandhowitwasusedanddissipated.Andyou'dhavetostudytrafficpatterns,workhabits,humaninteractionsandagreatmanyotherthingswedon'thavetimetotalkabouthere.Thenyou'dhavetotakeallthatdataandintegratethemtodevelopamodelcapableofpredictinghowthecityfunctions.Andit'sexactlythesameforbiologicalsystems.Wehavetogatherinformationatdifferentlevelsandfullyintegrateittoreallyunderstandhowsystemswork.4/161GenomeshighlighttheFiniteness

ofthe“Parts”inBiologyBacteria,

1.6Mb,~1600genes[Science

269:496]Eukaryote,13Mb,

~6Kgenes[Nature387:1]199519971998Animal,

~100Mb,~20Kgenes[Science

282:1945]Human,

~3Gb,~100Kgenes[???]?realthing,Apr‘00‘98spoof5/161大規模基因功效表示譜分析

伴隨人類基因組測序逐步靠近完成，人們自然會提出以下問題：即使我們已經取得了人完整基因圖譜，那我們對人生命活動能說明到什么程度呢？人們深入提出了一系列由上述數據所不能說明問題，比如：基因表示產物是否出現與何時出現；基因表示產物定量程度是多少；是否存在翻譯后修飾過程，若存在是怎樣修飾；基因敲除（knock-out）或基因過分表示影響是什么；多基因差異表示與表現型關系怎樣等等。概括這些問題，其實質應該是：知道了核酸序列和基因，我們依然不知道它們是怎樣發揮功效，或者說它們是怎樣按照特定時間、空間進行基因表示，表示量有多少。

6/161microarraysAffymetrixOligosDon’thavetoknowsequenceGlassslidesPatbrown7/1618/161功效圖譜FromCell,,V0l.104,3339/161基因組（Genome）轉錄組（Transcriptome）蛋白質組（Proteome）相互作用組（Interactome)定位組（Localizome）折疊子組（foldome）代謝組（Metabolome）表型組（Phenome）后基因組研究對象多層次遺傳圖譜（Geneticmap）限制性圖譜（Restrictionmap）物理圖譜（Physicalmap）功效圖譜（Functionalmaps）“快照”10/161后基因組時代對功效了解本質改變SPA序列結構功效ABCXYVZ相互作用網絡功效11/161研究思緒改變FromCell,,V0l.104,33312/161更加好整合生物過程不一樣階段分散數據.基因組+轉錄組+蛋白質組+代謝組滿足復雜查詢整合數據庫.對復雜生物過程更加好模擬.蛋白質折疊.復雜系統建模.Signaling/Metabolicpathways.Pathogenesis.生物過程動態研究.Fromthecomponentsofapathwaytothedynamicsofapathway.

功效基因組發展趨勢13/16114/161（二）、系統生物學研究一些例子15/161基因經過復雜多反饋網絡發揮作用復雜系統：一個病毒基因和開啟子相互作用網決定了它是休眠還是復制TRENDSINGENETICS5(2),67(1999)16/161

基因調控網絡模型Science15Jan1999,Vol28317/161哺乳動物細胞周期調控網絡(部分)。Mol.Biol.Cell10,2703–2734(1999).18/161AnnotatingtheYeastGenomeNetworkofyeastSup35proteinNetworkofyeastSIRprotein多信息融合蛋白質功效注釋（4NOV1999Vol402,

Nature)19/161半乳糖代謝通路研究（4MayVol292,

Science)基于已經有知識基本模型20/161整合轉錄組和蛋白質組試驗數據后取得精細功效圖譜21/161

諾貝爾獎得主

AlGilman主持小鼠心肌細胞鈣信號通路22/161E-cell剝離細胞由E-cell進行生物化學模擬ScienceApril2,1999,Vol28423/161系統生物學（SystemsBiology）成為近年主要研究方向TreyIdeker,etal,"IntegratedGenomicandProteomicAnalysesofaSystemticallyPerturbedMetabolicNetwork",4MayVol292Science

MichaelTLaub,etal,"GlobalAnalysisoftheGeneticNetworkControllingaBacterialCellCycle",15December,Vol290,Science

H.Jeong,etal."Lethalityandcentralityinproteinnetworks",Nature,Vol411,3MAYGeorgevonDassow,EliMeir,"Thesegmentpolaritynetworkisarobustdevelopmentalmodule",

Nature,Vol406,13JULY

H.Jeong,etal,"Thelarge-scaleorganizationofmetabolicsnetworks",Nature,v407,

ThomasSimonShimizu,etal,"MolecularmodelofalatticeofsignallingproteinsinVolvedinbacterialchemotaxis",NatureCellBiology,Vol2,

24/161MichaelB.Elowitz,etal,"Asyntheticoscillatorynetworkoftranscriptionalregulators``,Nature,v403,

S.Kalir,etal,"OrderingGenesinaFlagellaPathwaybyAnalysisofExpressionKineticsfromLivingBacteria",Science,v292,MatthewFreeman,"Feedbackcontrolofintercellularsignallingindevelopment",Nature,v408

ChunyanXu,etal,"OverlappingActivatorsandRepressorsDelimitTranscriptionalResponsetoReceptorTyrosineKinaseSignalsintheDrosophilaEye",Cell,Vol.103,

ThomasSurrey,FrancoisNedelec,"PhysicalPropertiesDeterminingSelf-OrganizationofMotorsandMicrotubules",ScienceVol29211MayNorbertFrey,etal,"DecodingcalciumsignalsinVolvedincardiacgrowthandfunction",NatureMedicine*Volume6*Number11*NovemberRekaAlbert,etal,"Errorandattacktoleranceofcomplexnetworks",Nature,v406,

25/161Nature

415,123-124()

26/161Nature

415,141-147()

27/161ModelingtheHeartfromGenestoCellstotheWholeOrgan

Sciences

Vol2951March28/161MolecularNetworks:TheTop-DownViewDennisBray

Science26Sep

Theexhilaratingprogressofthepastdecadehasbroughtan

unprecedentedwealthofquantitativeinformationonlivingsystems,

fromgenomicsequencestoproteinstructuresandbeyond.But

althoughtechnicaladvancesmakedatacollectionevereasier,

investigatorsareincreasinglyconcernedbytheirinability

togainabiggerpicture.Howcanthisgrowingmountainoffacts

beassimilated,andwherewillthenewideascomefromthat

willhelpusgainabroaderperspective?

Networks29/161（三）、系統生物學研究思緒30/161多信息融合構建功效圖譜FromCell,,V0l.104,33331/161FromCell,,V0l.104,33332/161系統生物學研究方法創新點生物復雜系統突現性規律，如鈣波功效基因組多層次系統貫通特征系統與系統，層次與層次相互作用新方法支持向量機主成份分析（時頻分析、偏最小二乘等）功效子系統建模多信息融合33/161EmergentPropertiesofNetworksofBiologicalSignalingPathwaysScience

15Jan1999,VOL28334/16135/161酵母細胞周期

表示譜分析

共調控基因Nature,,Vol405,1536/161大規模基因表示譜用于基因調控網絡構建37/161（四）、可能應用38/161腫瘤研究39/161腫瘤研究40/161心血管疾病研究41/16142/161SpectralAnalysisoftheProtein-proteinInteractionNetworkinBuddingyeast43/161Thetopologicalstructureinprotein-proteininteractionnetworkInclique,proteinsconnectquitetightly,almostinteractingwitheachother.However,ineachbipartite,proteinsweredividedintotwoparts,proteinsseldomconnectinsamepartsbutconnecttightlywithproteinsincounterpart.

AClique bBipartite44/161Thepercentageoffunctionclassesineveryclique

45/161FunctionpredictionforSSUprocessome

46/161Theprotein-proteininteractionnetwork:beforeandafterspectralanalysis

47/161

二、非編碼區功效研究48/161BREAKTHROUGHOFTHEYEAR():

Sciencecelebratesnineotherareasinwhichimportantfindingswerereportedthisyear,fromsubatomictoatmosphericandbeyond.

Firstrunner-up:RNAascending.

ShortRNAsclearlyplayimportantbiologicalroles.Dozensofthemoleculesarenowknowntoexistinthenematodeandfruitfly.ThecodingforthesemoleculesiscontainedintheDNAsequence.Some100ofthesetinyRNA"genes"havebeenfoundinthegutbacteriumEscherichiacoli,andsome200wereuncoveredinDNAfrommousebraintissue.Inthenematodeandfruitfly,theyseemtobeinvolvedindevelopment;inE.coli,theymayfacilitaterapidresponsestoenvironmentalchangeandcouldservesimilarfunctionsinmammals.49/161Whatisagenome?1911-gene:Elementaryunit,responsibleforthetransmissionofhereditarycharacters1920-genome:Setofgenesofanorganism 1944-Averyetal.DNAisthemoleculeofheredity1950-70:Doublehelix,GeneticcodeGenome=setofDNAmoleculespresentinacellandtransmittedtotheoffspring50/161AgenomeismorethanasetofgenesGenes(transcriptionunit):Protein-codinggenesRNAgenes:rRNAs,tRNAs,snRNAs,etc.UntranslatedRNAgenes(e.g.Xist,H19)Regulatoryelements(promoters,enhancers,etc.)Elementsrequiredforchromosomereplication(replicationorigins,telomeres,centromeres,etc.)Non-functionalsequencesNon-codingsequencesRepeatedsequencesPseudogenes51/161Genomesize52/161NumberofproteingenesHumanvsE.coli:Genomesize:x1000Numberofgenes:x1053/161Proportionoffunctionalelementswithingenomes54/161Functionalelementsinthehumangenomenon-translatedRNAgenes:Xist,H19,His-1,bic,microRNAs,etc.Regulatoryelements:promoters,enhancers,etc.Transposableelements(LINEs,SINEs,...):40-45%86%no(known)functionintergenicDNA60-70%Introns25%Codingregions(proteins)1.7%tRNA,rRNA,…0,5%SatelliteDNA(centromeres,telomeres)12%3.4109nt30000-40000proteingenes55/161RepeatedsequencesTandemrepeatsSatelliteMinisatelliteMicrosatelliteInterspersedrepeatsDNAtransposonsRetroelements56/161Tandemrepeats motif blocsize %human genomesatellite: 2-nt upto10Mb 10%minisatellite: 2-64nt 100-20,000bp ?microsatellite: 1-6nt 10-100bp 2%SlippageoftheDNApolymerase:CACACACACACAUnequalcrossing-over:57/161Centromeres,telomeres:

SatelliteDNA58/161InterspersedrepeatsTransposableelements(autonomousornon-autonomous):DNAtransposons(rareinmammals)Retroelements59/161RetroelementsLINEs(longinterspersedelements):6-8kbretroposonsSINEs(shortinterspersedelements):80-300bpsmall-RNA-derivedretrosequences(tRNA),polIIIEndogenousRetroviruses:1.5-10kb60/16161/161FrequencyoftransposableelementsinthehumangenomeTotal=42%(Smit1999)Probablyunderestimated62/161Thefrequencyoftransposableelementsisnotuniformalongthehumangenome:

e.g.inter-chromosomicvariations

(Smit1999)63/161PseudogenesAfterageneduplication:evolutionofnewfunction(sub-functionalizationorneo-functionalization)orgeneinactivation64/161Retropseudogenes65/161Retropseudogenes23,000to33,000retropseudogenesinthehumangenomeOftenderivefromhousekeepinggenes66/161非編碼區功效研究是最挑戰性課題Whatisthetotalnumberofhumangenes?

28,000±4,000

Only1.1%ofthegenomeisspannedbyexons,whereas24%isinintrons,with75%ofthegenomebeingintergenicDNA.

Oneofthelargestchallengesisidentifyingtheunknownfunctionsthatalmostcertainlyexistinmuchofthe“junk”DNA.67/161OrganismYearMillionsTotalPredictedNumberofgenesofbasescoveragenumberpermillionbasessequenced(%)ofgenessequenced

Humangenomeroughdraft2,6938431,78012(publicsequence)Humangenomeroughdraft2,6548339,11415(Celerasequence)Humanchromosome2134752257

Humanchromosome221999347054516

Arabidopsisthaliana

1159225,498221

Drosophilametanogaster1166413,601117

Caenorhabditiselegans

1998979919,099197

Saccharomycescerevisiae

199612935,80048368/161

CodingDNA:1~1.5%

NoncodingDNA:

intron24%

intergenicDNA75%

promoter

telomeres

repetitive45%

LINE21％850,000（拷貝數）

SINE13％1,500,000

LTR8％450,000

Transposons3%300,000

Noncodingandnonrepetitive

35%

LINEplayacrucialroleinXinactivation,theprocessbywhichoneofthetwoXchromosomesinafemaleisturnedoffearlyindevelopment.

SmallRNA

69/161

重復序列在基因組中百分比

Human45%

Arabidopsis11%

C.elegans7%

D.melanogaster3%

70/161Mammaliangenomes:summaryGenes,regulatoryelements:~2%Non-codingsequences:~98%SatelliteDNA(centromeres)~10%Microsatellites~2%Transposableelements~42%Pseudogenes~1%Other(ancienttransposableelements?)~43%Variationsingeneandrepeatdensityalongchromosomes71/16172/161Genenumbersdonotincreaseasmuchasexpectedwithcomplexity:

-wormandflygenenumbers(12-14,000)areonlyabouttwice thoseofyeast(6,000)andP.aeruginosa(5,500) -mammalian(human,mouse)genenumbers(~30,000)areonly abouttwicethoseofinvertebrates.ThecomplexityproblemThissuggeststhat: - animalshave

arelativelystablecoreproteome,whose componentsaremultitasked

indifferentiationanddevelopment - variationsinphenotypeoccursmainlybyvariationinthecontrol architecture(unlikeprokaryotes)Phenotypicvariationinmammalsisprimarilyassociatedwithnoncodingregions:

-only~10,000outof~3,000,000polymorphismsbetween individualhumans(0.3%)occurinproteincodingsequences -only1%ofgenesaredifferentbetweenhumansandmice.98%oftranscriptionaloutputinhumansisnoncodingRNA73/161ExcisedintronsandothernoncodingRNAsappeartoberelativelystable

(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,all7are developmentallyregulatedandallhavegeneticsignatures74/161一、NoncodingRNA功效例子75/161SINEelementsserveasrecombinationhot-spotsallowingtheexchangeofgeneticmaterialbetweenunrelatedsequences.

SINEsastranslatedpartsofhostgenes

76/161SINEsasasourceofregulatoryelements

Theinsertionofarepetitivesequenceintoagenecaninfluenceitstranscription.TheSINEsandotherrepeatscanactastissue-specificenhancersorsilencersoftheadjacentgenes.Steineretal.showedthatinthechickenlysozymegene,aCR1elementlocatedupstreamofthecodingregionactsasatranscriptionalsilencer.SafferandThurstonshowedthatanegativeregulatoryelementofthe7.02bidirectionalpromoterinthe"Africangreenmonkey"ispartofanAlusequence.ThehumanCD8ageneisregulatedinT-cellsbyanenhancerlocatedinthelastintron.The5'partoftheenhancerconsistsofafullAluelementinsertedinthesenseorientation.AnL1elementlocatedabout3kbupstreamoftheratinsulin-1geneactsasasilencer,77/161X-inactivationisthemammaliandosagecompensationmechanism,usedtoequalizeX-linkedgenedosagebetweenmaleandfemalecells.InmammalsdosagecompensationoccursbythetranscriptionalsilencingofoneXchromosomeinallfemalesomaticcells.

ThesilencingoftheinactiveXchromosomeisachievedbyanXchromosomewidealterationinchromatinstructure,fromactiveeuchromatintoinactiveheterochromatin.X-inactivationisnucleatedandbidirectionallypropagatedfromtheX-inactivationcenter.TheXistgenelieswithintheX-inactivationcenterandisrequired

toinitiateXchromosomeinactivation.

Xistencodesalarge,spliced,polyadenylated,noncodingRNAthatisexpressedexclusivelyfromtheotherwiseinactiveXchromosome.

CytologicallyXistRNAappearsasaclusterofparticlesthatcoattheinactiveXchromosome.SpreadofXistRNAcorrelatestemporallywiththespreadofsilencingalongtheXchromosome.ThetwomostinterestingquestionsthatarisefromthischaracterizationofXistare:howdoesXistRNAfunctioninalteringchromatinstructureandhowisXistitselfregulated?

/pibs/faculty/panning.htmlBarbara

PanningLab78/161SmallRNAandRNAInterference(RNAi）

AnumberofrecentreportshaveshownthatsmallRNAmoleculesplaysignificantrolesinbothgenesilencingandregulationofdevelopmentaltiming.Small,processeddouble-strandedRNAs(alsocalledshortinterferingRNAsorsiRNAs)mediatethephenomenonknownasRNAinterference(RNAi)—post-transcriptionalgenesilencing(PTGS)inducedbytheintroductionofdsRNA—andhavebiologicalrolesinviralresistanceinplantsandtransposonsilencinginCaenorhabditiselegans.AnothergroupofsmallRNAmolecules,knownassmalltemporalRNAs(stRNAs),regulatesC.elegansdevelopmentaltimingthroughtranslationalrepressionoftargettranscripts.

InRNAi,dsRNAintroducedintosusceptibleorganismsisprocessedinto~22nucleotide(nt)siRNAs.These22ntsiRNAssubsequentlybindtothehomologousregionoftheirtargettranscriptandtagitfornucleasecleavage.ThusgenesilencingiseffectedbydestructionofthetargetmRNA.79/161TimelineLate70’s–lin-4andlet-7regulatedevelopmentaltiminginworm1993–lin-4codesfora~22ntRNA,complementaryto3’UTRoflin-14–….sodoeslet-7(stRNAs)–let-7isconservedinbilaterallysymmetricanimals–~100miRNAsdiscoveredbycloninginworm,flyandhuman–miRNAsconservedinplants–Sciencemagazine’sbreakthroughoftheyear–miRNARegistryestablished–miRNAsmayaccountfor1%oftotalgenecountinanimals–afewtargetsofmiRNAsidentified–miRNARegistryhas719miRNAs80/161

長久以來人們一直認為RNA分子主要作用是與蛋白質合成相關，不論是tRNA,rRNA還是mRNA，它們一起組成一套精密機構將DNA中基因信息傳遞到蛋白質。但自上世紀九十年代以來對小片段RNA研究一系列新發覺，使人們不得不重新認識RNA在生命活動中主要作用。其中最突出例子是由研究基因緘默現象（GeneSilencing）而造成RNA干涉（RNAInterference，RNAi）發覺。轉錄后基因緘默（Post-transcriptionalgenesilencing，PTGS）,最早發覺存在于矮牽牛和少數幾個植物當中。這種特殊現象表現為，當對這些植物進行轉基因后，導入基因和其相同內源基因同時都被抑制。深入試驗表明同源轉錄本確實出現過，不過很快被降解了。對這一現象深入研究開始于上世紀九十年代。當初一些科學家以線蟲（Caenorhabditiselegans）為對象探討用反義RNA去阻斷基因表示，結果反義RNA確實能夠阻斷基因表示，不過奇怪是，作為對照正義鏈RNA也一樣阻斷了基因表示。今后另一些科學家以同時包含正義鏈和反義鏈雙鏈RNA（double-strandedRNA，dsRNA）去阻斷基因表示，結果表現出比單獨注射正義鏈或者反義鏈都要強得多基因緘默現象。這種由RNA造成基因緘默現象被稱為RNA干涉（RNAinterference,簡稱RNAi）。

81/161

對RNA干涉機制研究發覺：dsRNA一旦進入細胞內，就會被一個稱為Dicer特定酶切割成為21-23核苷酸長小分子干擾RNA（smallinterferingRNAs，siRNA）片段，Dicer酶屬于RNaseIII家族中能特異識別雙鏈RNA組員，它以ATP依賴方式切割由外源導入或者由轉基因、病毒感染等各種方式引入雙鏈RNA。切割產生siRNA片段隨即

與一些酶結合成為誘導緘默復合體（RNA-inducedsilencingcomplex，RISC）。激活RISC經過堿基配對定位到與siRNA同源mRNA轉錄本上，并在距離siRNA3'端一定位置上切割該mRNA。這么就使與此mRNA對應特定基因成為緘默狀態。繼線蟲之后，在果蠅中也發覺了RNA干涉。現大量研究已表明，RNA干涉廣泛存在于從真菌到植物、從無脊椎動物到晡乳動物各種生物中，甚至也存在于低等原核生物中。從遺傳學、分子生物學和生化學角度進行研究也指出轉錄后基因緘默（PTGS）和RNA干涉可能在生命進化早期就存在。有些人提出轉錄后基因緘默可能是進化過程中一個抵抗轉座子或RNA病毒防御機制，是生物使用一個古老抗病毒策略，可能在植物和動物分化之前就已經出現。

82/161miRNAbiogenesisAdaptedfromDPBartel,Cell116:281-297()83/161

上世紀九十年代美國Dartmouth醫學院VictorAmbros小組研究結果表明，其實這么RNA就存在于生物體本身。他們以線蟲為對象用基因打靶技術研究一些基因對其發育影響。他們找到了一個對發育有顯著干擾基因。通常線蟲要經過四個幼蟲階段才能成熟，這個基因突變使其只停留在第一階段。令人們驚奇是這個基因并不編碼任何蛋白質，而是編碼一個小RNA。以后研究證實，這么小RNA基因在果蠅、軟體動物、魚類以及人體中都存在。有研究報道在大腸桿菌中已經發覺幾十個小RNA基因，在小鼠腦組織中發覺了200多個小RNA基因。現在科學家們正系統地在各種生物中尋找小RNA基因。

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小RNA和RNA干涉研究含有廣泛應用前景，有科學家認為它有可能掀起一場生物革命。首先RNAi是一項快速、高效、便于操作使靶基因失活技術。所以它能夠象基因敲除一樣非常有效地判定特定基因功效。伴隨各種模式生物體基因組計劃完成，生物學家們已經能夠方便從數據庫中取得全基因組序列，從而找到研究者感性趣基因序列，據此設計出dsRNA就能夠使該基因緘默。這是研究疾病機理和判定候選藥靶關鍵步驟，也為未來可控地打開或者關閉某一特定基因這一目標奠定了基礎。現已經有兩個研究組使用了RNAi技術分別對兩條線蟲染色體上全部基因進行大規模功效研究，并正在利用該技術對線蟲全基因組進行研究。RNA干涉也為疾病治療開辟了新路徑。RNA干涉理論上能降低肝炎病毒感染所需蛋白質，而到達降低病毒數量目標；也能夠用來降低一些遺傳疾病不正常基因蛋白質制造量，以治療該疾病。比如，多谷胺酸聚合疾病，包含脊髓小腦運動失調癥和亨庭頓氏癥。甚至能夠經過抑制病毒或HIV本身信使RNA來抵抗病毒感染尤其是HIV感染。

85/161治療SARSRNAi設計NumbersofeligiblesiRNAcandidatetargetsselectedbasedontheoreticaldesign

1)Correspondingproteins:proteinscodedbythegenewheretargetsequencesposition.

CorrespondingProtein1)

NumberofcandidatetargetsRNApolymerase264S46E3M6N2986/161SequencesofseveralrepresentativesiRNAcandidatetargetsCorrespondingproteins1)

SequencesofsiRNAcandidatetarget(5’-3’)Positionof5’end2)

RNApolymeraseAACGAGAAAACACACGTCCAA289RNApolymeraseAAACGTTCTGATGCCTTAAGC478RNApolymeraseAAATGGACGGCATTCAGTACG536SAAGCTCCTAATTACACTCAAC21568SAATCATACGTTTGGCAACCCT21708SAACAACAAGTCACAGTCGGTG21813EAAGAAACAGGTACGTTAATAG26136EAAAACCAACGGTTTACGTCTA26272EAACCAACGGTTTACGTCTACT26274MAACGGTACTATTACCGTTGAG26407MAACTCCTGGAACAATGGAACC26438MAATGGAACCTAGTAATAGGTT26450NAATGGACCCCAATCAAACCAA28129NAACCAGAATGGAGGACGCAAT28201NAATAATACTGCGTCTTGGTTC282611)Correspondingproteins:proteinscodedbythegenewheretargetsequencesposition;2)Positionof5’end:the5’endpositionofsiRNAcandidatetargetssequencerelativetoSARS-CoVgenome.

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小RNA研究又取得了新進展。幾組科學家研究了酵母和四膜蟲這兩種生物體中RNA干擾現象，他們發覺小RNA對染色質形狀有著極大控制作用。即，小RNA能夠永久性關閉或刪除一部分DNA（其機制現在還不了解），而不只是簡單地使DNA暫時緘默。冷泉港試驗室ShivGrewal、RobertMartienssen等發覺缺失日常小RNA裂殖酵母細胞不能在中心粒正確形成異染色質，從而破壞了正常細胞分裂。弗吉尼亞大學DavidAllis等和羅切斯特大學MartinGorovsky等也發覺，小RNA能引發四膜蟲（Tetrahymena）細胞分裂期間DNA缺失或序列重組。這些新發覺只是小RNA研究領域一小部分，科學家們正試圖確定成百種小RNA各自功效；確定哪些物種含有哪類小RNA以及它們在該物種中行為是什么？

小RNA出現重新喚起了科學家們對“RNA世界”重視及對“生命起源于RNA分子”這一命題興趣。有科學家認為成千上萬非編碼蛋白質RNA分子組成了巨大分子網絡調整著細胞中生命活動，它們與蛋白質-蛋白質相互作用網絡相對應，好比宇宙學中暗物質，將為基因組和生命科學研究提供無比美好前景。

88/161miRNAstargetsDPBartel,Cell116:281-28789/161C.elegansA.thalianaStructuraldifferencesadaptedfromDavidBartel90/161SecondarystructureparametersThemiRNAshouldbepartofacontinuoushelixTheminimumfreeenergyvalueshouldbelessthan-30Kcal/molTheminimumnumberofpairedresiduesinthemiRNAshouldbe15themaximumnumberofunpairedresiduesinboththemiRNAcodingandcomplementarystrandshouldbe5.themaximumnumberofG:UpairsinthemiRNAshouldbe5

91/16192/161Fig.1.ComputationalidentificationofvertebratemiRNAgenes.MiRscanidentified188humanloci81(red)of109knownhumanmiRNAs14(pink)paralogsofknownmiRNAs38(purple)foundinzebrafishlibrary55experimentallyunverifiedUpperboundof255miRNAsinhuman

81/109=0.74sensitivity 188/.74=255total93/161/PLANTncRNAs/

Wehavecollectedexistingdataonplant

noncodingRNAsandexpandedonthisbyexaminingabout20,000ArabidopsisESTsforcharacteristicsofnoncodingRNAs.

About15putativeArabidopsisncRNAshavebeenreportedintheliteratureorhavebeenannotated.

Severalhavehomologsinotherplants,butallappeartobeplant-specificwiththeexceptionofSRPRNA.

Conversely,noneofabout30ncRNAsreportedfromyeast,bacteriaoranimalsystemshavehomologsinArabidopsis.

NoncodingRNAinPlants94/161RegulationofTranscriptionbyaSmallNuclearRNA

/hottopics/7SK_010702.html

Ineukaroyticcells,transcriptionisregulatedbyahostoftranscriptionfactors.TheP-TEFbcomplex,composedoftheCDK9kinaseandcyclinT1/T2proteins,isanexampleofageneraltranscriptionfactorthatmayhavearoleinbothtranscriptioninitiationandelongation.ThiscomplexmodulatesmRNAtranscriptionbyphosphorylatingthecarboxy-terminaldomain(CTD)ofRNApolymeraseII(RNApolII).Twopaperspublishedinthe15NovemberissueofNaturesuggestthattheactivityoftheP-TEFbcomplexisregulatedbythe7SKsmallnuclearRNA(snRNA),anabundant330ntnuclearRNAofpreviouslyunknownfunction(2,3).Thetworesearchteamsshowedthat7SKRNAcouldbindtothepTEFbcomplex,sequesterthecomplex,andinhibititskinaseactivity.95/16196/161snoRNABackgroundSmallnucleolarRNA:snoRNA（sRNAinArchaea,scaRNAincajalbody)2.Fungi,protists,plants,animals,prokaryoticarchaea3.Number:75~100(yeast)——200（mammals)4.Length:60~300nt5.Genomicorganization:intronicorindependent97/161StructureTheboxC/DfamilyTheboxH/ACAfamilyC/D-H/ACAhybrid(U85,U87,U88,U89)RNAcomponentforRNaseMRP(StructuresimilartothatofRNaseP)98/16199/161

tmRNA-定義是存在于細菌一類穩定smallRNA。tmRNA同時具備類似mRNA和tRNA功效。當前認為它是細菌體內蛋白質合成中起“質量控制”物質基礎之一。100/161tmRNA功效介紹tmRNA功效:(1)將“滯留”在mRNA上核糖體解脫下來.(2)將一段信號肽加在有缺點蛋白質C末端,使其有效水解。

101/161102/161tRNA參加蛋白質生物合成中至關主要兩個功效上相連生物化學事件。一是由氨基酰-tRNA合成酶(aaRS)催化tRNA氨基酰化(tRNA個性)，經過aaRS對tRNA序列和結構元件專一識別和氨基酰化，使tRNA轉化為氨基酰tRNA。二是氨基酰tRNA在核糖體上提供氨基酸，它由tRNA反密碼子與mRNA密碼子經過互補堿基配對而發動。這兩個事件有序而協同進行，決定了每個蛋白質氨基酸序列

103/161snRNAOverviewSmallnuclearRNA(snRNA)isthenameusedtorefertoanumberofsmallRNAmoleculesfoundinthenucleus.TheseRNAmoleculesareimportantinanumberofprocessesincludingRNAsplicing(removaloftheintronsfromhnRNA)andmaintenanceofthetelomeres,orchromosomeends.104/161Spliceosomespliceosomalprotein>50spliceosomalRNA~7U1,U2,U4,U5,U6,U7,U12105/161Biologicalfeatures一級結構不保守二級結構保守RNA聚合酶II(U6RNA聚合酶III)種類少各個物種各種snRNA都有發覺106/161U1107/161U2108/161U4109/161U5110/161U6111/161U7112/161U12113/161114/161PackagingRNA

(pRNA)115/161pRNAfunctionThepRNAmoleculesinteractintermolecularlyviahand-in-hand