1820Regulatory RNAs and Genome AnalysisRNA调控和基因组分析.docx
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1820Regulatory RNAs and Genome AnalysisRNA调控和基因组分析.docx
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1820RegulatoryRNAsandGenomeAnalysisRNA调控和基因组分析
RegulatoryRNAs
Chapter18
I.RegulatoryRNAs
A.RegulationbyRNAsinBacteria
B.RNAInterferenceinEukaryotes
C.SynthesisandFunctionofmiRNAs
D.RNAiasaToolforRegulatingGeneExpression
E.RegulatoryRNAsandX-Inactivation
F.RNAiandHumanDisease
G.Post-transcriptionalRegulation
H.FeedbackInhibition
II.GenomeAnalysis
A.DNAmicroarrays
B.IdentificationofRegulatoryDNASequences
III.SystemsBiolog
A.RegulationbyRNAsinBacteria
FormanyyearsscientistshaveknownthatsmallRNAmoleculesregulategeneexpressioninbacteria.
SomesmallRNAmoleculesregulatetranscription.
Forexample,the6SRNAinE.colibindstotheσ70subunitofRNApolymerase.
Whatroledoessigmaplayintranscription?
σ(sigma)actsasaspecificityfactor.ItspecificallybindstopromotersequencesintheDNA.
The6SRNAbindstoσ70andreducestranscriptionatmanyofthepromotersthatσ70bindsto.Therearelargeramountsofthe6SRNAduringthestationaryphaseofcellgrowth.
Thereare3phasesinbacterialcellgrowth:
1.lagphase
2.exponentialphase
3.stationaryphase
Activelydividingbacteriaareintheexponentialgrowthphase.Afterthenumberofcellsintheculturegetstoohigh,thegrowthslowsandcellsenterthestationaryphase.Bacteriathataretakenfromthestationaryphaseandplacedinfreshmediawillgrowquicklyagain,butonlyafteraninitiallagphase.
Thecellsmakemore6SRNAduringthestationaryphaseofgrowth.DuringthestationaryphaseadifferentσfactorisproducedcalledσS.σSbindstodifferentpromotersthanσ70.Thesepromotersareingenesthathelpthecellssurvivethestressofthestationaryphase.
The2σfactorscompetewitheachothertobindtothecoreRNApolymerase.
Thus,the6SRNAhelpsthecellstoshiftfromexpressinggeneswithpromotersboundbyσ70thatareneededduringexponentialgrowth,toexpressinggeneswithpromotersthatareboundbyσSthatareneededduringstationaryphase.
ThereisanothergroupofsmallRNAsinbacteriathatregulatetranslationandmRNAdegradation.TheyarecalledsmallRNAsorsRNAs.
Theyareabout80-110basepairslong.
E.colihasnearly100sRNAs.
About12ofthesRNAsinE.colihavebeenwellstudied.
MostbasepairwithcomplementarysequencesintargetmRNAs.ThiscausesthedegradationofthemRNA,orinhibitsitstranslation.Thoughinsomecasesitcanactuallyincreasetranslation.
BindingofasRNAinhibitstranslationbyblockingtheribosomebindingsite.
BindingofthesRNAactivatestranslationbyfreeingaribosomebindingsite.
B.RNAInterferenceinEukaryotes
InRNAinterference(RNAi)veryshortRNAsrepressexpressionofcertaingenes.
TheshortRNAscaninhibittranslation,causethedegradationofthemRNA,orrepresstranscriptionofthegene.
ScientistscanusethesesmallRNAstosilenceorturnoffexpressionofagene.ThismakestheseRNAsapowerfultoolforresearch.
SmallRNAsmadebyscientistsforgenesilencingarecalledsmallinterferingRNAsorsiRNAs.
ThesmallRNAsproducednormallybycellsarecalledmicroRNAsormiRNAs.
miRNAsareproducedfromlongerRNAmoleculesandthentheyarecutbyDicer.
DicercutsthelongermRNAsintoshortpiecesabout21-23basepairslong.
DicercutsboththenaturallymademiRNAsandalsocutsthesmallinterfering(siRNAs)thatareaddedbyscientists.
ThemiRNAsandsiRNAsinhibitexpressionofgenesin3ways:
1.TheycausedegradationofthemRNA
2.TheyinhibittranslationofthemRNA
3.Theycausemodificationsinthechromatintosilenceitstranscription.
ThemiRNAsorsiRNAsbindtoaRNA-inducedsilencingcomplex(RISC).
TheRNAisdenatured.OnestrandiscalledtheguideRNAandtheotheristhepassengerRNA(whichisusuallydiscarded).
TheRISCbindstotargetmRNAswiththeguideRNA.ThetargetmRNAsaredegradediftheirRNAiscloselycomplementarytotheguideRNA.Ifthesequencesarenotascomplementary,translationofthetargetmRNAwillbeinhibited.
TheRISCcanalsoenterthenucleuswhereitcanrecruitotherproteinsthatmodifythechromatinnearthepromoterofthegenethatiscomplementarytotheguideRNA.Thiswillstoporsilencetranscriptionofthegene.
UsingRNAitosilencegenesisveryefficient.OftenonlyverysmallamountsofdsRNAareenoughtocompletelystopexpressionofatargetgene.ThisispartlybecausetheRISCcandegrademanymRNAs.
C.SynthesisandFunctionofmiRNAs
miRNAshaveacharacteristicstructurethatmakesthemeasytoidentify.
FirstalongerRNA,calledapri-miRNA(priforprimary)istranscribed.Thisformsahairpinstructure.Thisiscut2times.Thefirstcutreleasesthestemloop,whichiscalledthepre-miRNA.
Structuresofsomepre-miRNAs.
Thepre-miRNAscanproduce2regulatorymiRNAs,onefromeachsideofthestemloop.
Structuresofsomepre-miRNAs.
Thepre-miRNAscancomefrombothintronsequencesandexonsequences.
Thedistinctivesecondarystructure(stemloop)ofthepre-miRNAsmakesitpossibletofindthesesequencesbyscanningthegenome.Insomecasesitisalsopossibletopredictwhichtargetgeneswillberegulatedbasedonthesequencecomplementarity.
1.Drosha
DroshaisanRnaseIIIenzymethatcutsthepri-miRNAtwicetoreleasethestemloopstructureofthepre-miRNA.
DroshabindstoDGCR8(alsocalledPasha)toformthemicroprocessorcomplex.Thisbindstothepri-miRNA.Itreleasesthestemloopwhichincludesabout65-70basepairs.Thisisthepre-miRNA.
CleavagebyDroshaoccursinthenucleus.Itcutsbothstrandsofthepri-miRNAtoproducethepre-miRNA.
Droshadoesnotrecognizeaspecificsequence,butrecognizesthestem-loopstructure.Itbindstothestemandthesingle-strandedRNAbelowthestems.
Itleavesa2basepairoverhangonthe3’endofthedouble-strandedRNA.
2.Dicer
Thepre-miRNAmovesfromthenucleustothecytoplasm.HereDicercutsthe
pre-miRNAtoproducethemiRNA,whichis21-25basepairslong.
Dicerboundtodouble-strandedRNA.
3.RISC
Thedouble-strandedmiRNAproducedbyDicerbindstotheRNA-inducedsilencingcomplex(RISC).ThentheRNAisdenaturedtoproducetheguideRNAandreleasethepassengerstrand.
TheRISCwiththeguideRNAisnowreadytobindandcutorslicecomplementarymRNAs.
RISCisacomplexofmanyproteins.ItincludesaproteinfromtheArgonautefamilyofproteins.TheArgonauteproteinhasRNaseactivityandisoftencalledtheslicer.Thus,mRNAcuttingisoftencalled“slicing”.
ManyorganismshavemorethanonekindofArgonauteprotein.Humanshave8membersoftheArgonautefamiliyofproteins.NotallthemembersoftheArgonautefamilyhaveslicer(RNase)activity.RISC’swithnonslicingArgonautesmayinhibittranslation.
ThemechanismforhowtheRISCinhibitstranslationisnotaswellunderstood.ItispossiblethatthemRNAsaremovedtoprocessingbodies(Pbodies)inthecytoplasm.Thisinhibitstranslation.
BindingofanmiRNAtoanmRNAcanalsodegradethepolyAtailofthetargetmRNA.Thisalsoinhibitstranslation.
4.GeneSilencingthroughChromatinModification
HowmiRNAssilencegeneexpressionthroughmodifyingthechromatinhasbeenbeststudiedinSchizosaccharomycespombe(S.pombe).Thisisafissionyeastthathasbeenextensivelystudied.
S.pombewasisolatedfromAfricanbeerin1893.ItsnamecomesfromtheSwahili(Africanlanguage)wordforbeer,whichispombe.
Itisasinglecelledeukaryote.Thecellsarerod-shaped.
InS.pombetheareasofthegenomethatarenearthecentromeresaresilenced.Thissilencingisthroughhistonemodifications.
ThecentromeresinS.pombehaveacentralpartthatisuniquesequences.Oneachsideofthistherearerepeatedsequencesthatarepresentinallcentromeres.
HistonesboundtotheDNAnearthecentromereshavelowlevelsofacetylationandmethylationofthelysineatposition9ofthetailonhistone3.ThisrepressestranscriptionofthisDNA.
RNApolymerasetranscribesbothstrandsofthecentromericrepeatsequences.Thesehybridizetoformdouble-strandedRNAs.ThesebecomepartofaRISC-likecomplexcalledRITS(RNA-inducedtranscriptionalsilencing).
TheRNAintheRITSbindstocomplementarysequencesthatarebeingtranscribedbyRNApolymerase.ThisrecruitsSwi6andCir4tothesequenceandtheymodifythehistonetails.TheRITSalsoslicestheRNAthatisbeingtranscribedbyRNApolymerase.
D.RNAiasaToolforRegulatingGeneExpression
RNAiisextremelyusefulforstudiesinthewormC.elegans.Thewormsfeedonbacteria(E.coli)andthisworksasamethodfortransportingthedsRNAintothecellsoftheworm.
TheDNAcanbeclonedintoaplasmidvector.Thenwithtransformation,thiscanbetransferredintoE.colibacteria.The
E.colibacteriawilltranscribetheDNAtoproducethedsRNAthatcansilencegenesinC.elegansafterthewormseatthebacteria.
TherearelibrariescontainingdsRNAtosilenceanygeneintheC.elegansgenome.Theselibrariescanbescreenedtotestwormsfortheresultsofturningoffanygeneinthegenome.
E.colicellsproducethedsRNAsthatwillsilencegenesintheworms.
Scientistshavedesignedandsynthesizedoligonucleotidesthatcanbeclonedintoplasmids.Whentheshortgeneistranscribed,itwillfoldintoastemloopstructurethatwillberecognizedandcutbydicer.ThesearecalledshorthairpinRNAs(shRNA).
UsingshRNAsanygeneinthegenomecanbetargetedandsilenced.
AlibraryofgenescanbetestedwithplasmidsthateachcontainadifferentshRNA.Thesecanbetransferredintocellstoseewhatphenotypesoccur.
E.RegulatoryRNAsand
X-Inactivation
InmammalsfemalesareXXandmalesareXY.Havingtwiceasmuc
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