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RegulationofHomologousRecombinationinEukaryotesWolfDietrichHeyerKirkTEhmsenandJieLiuDepartmentofMicrobiologyUniversityofCaliforniaDavisDavisCalifornia956168665emailwdheyerucdaviseduDepart ID: 102809

RegulationofHomologousRecombinationinEukaryotesWolf-DietrichHeyer KirkT.Ehmsen andJieLiuDepartmentofMicrobiology UniversityofCalifornia Davis Davis California95616-8665;email:wdheyer@ucdavis.eduDepart

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GE44CH06-HeyerARI3October201011:50 RegulationofHomologousRecombinationinEukaryotesWolf-DietrichHeyer,KirkT.Ehmsen,andJieLiuDepartmentofMicrobiology,UniversityofCalifornia,Davis,Davis,California95616-8665;email:wdheyer@ucdavis.eduDepartmentofMolecularandCellularBiology,UniversityofCalifornia,Davis,Davis,California95616-8665 Annu.Rev.Genet.2010.44:11339FirstpublishedonlineasaReviewinAdvanceonAugust6,2010AnnualReviewofGeneticsisonlineatThisarticlesdoi:2010byAnnualReviews.AllrightsreservedKeyWordscyclin-dependentkinase,DNAdamageresponse(DDR),DNArepair,phosphorylation,sumoylation,ubiquitylationHomologousrecombination(HR)isrequiredforaccuratechromosomesegregationduringtherstmeioticdivisionandconstitutesakeyre-pairandtolerancepathwayforcomplexDNAdamage,includingDNAdouble-strandbreaks,interstrandcrosslinks,andDNAgaps.Inaddi-tion,recombinationandreplicationareinextricablylinked,asrecombi-nationrecoversstalledandbrokenreplicationforks,enablingtheevo-lutionoflargergenomes/replicons.Defectsinrecombinationleadtogenomicinstabilityandelevatedcancerpredisposition,demonstratingaclearcellularneedforrecombination.However,recombinationcanalsoleadtogenomerearrangements.Unrestrainedrecombinationcausesundesiredendpoints(translocation,deletion,inversion)andtheaccu-mulationoftoxicrecombinationintermediates.Evidently,HRmustbecarefullyregulatedtomatchspeciccellularneeds.Here,wereviewthefactorsandmechanisticstagesofrecombinationthataresubjecttoregulationandsuggestthatrecombinationachievesexibilityandro-bustnessbyproceedingthroughmetastable,reversibleintermediates. GE44CH06-HeyerARI3October201011:50 recombination(HR):betweenidenticalornearlyidentical Homologousrecombination(HR)isakeypath-waytomaintaingenomicintegritybetweengenerations(meiosis)andduringontogenicde-velopmentinasingleorganism(DNArepair).Atypicaldiploidhumancellneedstomaintainabout6basepairsinthecorrectsequenceandchromosomalorganization,aformidabletaskthatisusuallyperformednearlyperfectlyfromonesomaticcellgenerationtothenext(44).RecombinationisrequiredfortherepairortoleranceofDNAdamageandtherecoveryofstalledorbrokenreplicationforks(95).How-ever,recombinationisalsopotentiallydanger-ousasitcanleadtogrosschromosomalrear-rangementsandpotentiallylethalintermediates(89).Notsurprisingly,defectsinHRandasso-ciatedprocessesdeneanumberofhumancan-cerpredispositionsyndromesassociatedwith DNAREPAIRPROTEINSANDHUMANGENETICDISEASEDefectsinDNArepairproteinsleadtovariousinheritedhu-mandiseasessharingcommonfeaturessuchasgenomeinstabil-ityandcancerpredisposition(71).MutationsofseveralRecQhelicases,BLM,WRN,andRecQ4,causeBloom,Werner,andRothmund-Thomsonsyndromes,respectively.TheothertwoRecQhelicases,RECQ1andRECQ5,havenotyetbeenimplicatedinhumandisease,butcellularstudiesdemonstratethattheyfunctioningenomemaintenance.Fanconianemia(FA)isanautosomalrecessivedisordercharacterizedbypro-gressivebonemarrowfailure.MutationsingenesaffectDNAinterstrandcrosslinkrepair;amongthem,areinvolvedinHR.aremajorbreastandovariantumorsuppressorgenesandbothfunctioninHR.DefectiveATM,akeysensorkinaseintheDDRpathway,leadstoataxiatelangiectasia(A-T),aneurodegenerativediseasewithseverephysicaldisabilities.MutationsofintheMRNcomplexcausesimilardiseases,A-TlikedisorderandNijmegenbreakagesyndrome,respectively.Mutationsim-pairingDNAmismatchrepairresultinhereditarynonpolyposiscolorectalcancer(HNPCC),anautosomaldominantdiseasewithhighlyelevatedriskforcoloncancer.genomeinstability(seesidebar,DNARepairProteinsandHumanGeneticDisease).Howdoesthecellachievethebalancebetweentoolittleandtoomuchrecombination?Theremustberegulationandtheanswerwilldependontheorganism,celltype,cell-cyclestage,chro-mosomalregion,aswellasthetypeandlevelofgenotoxicstress.HRinmeiosisissubjecttospecicregula-tionthattargetsrecombinationeventstoho-mologs,establishingcrossoveroutcomestoas-sistinmeioticchromosomesegregation(46,76).Inaddition,thisvolumecontainsadedi-catedreviewontheRecQhelicases,whichpro-videsamuchmorecomprehensivediscussionofthisimportantclassofproteinsthancanbeachievedhere(15).DuetospacelimitationswereferthereadertorecentreviewsonhowmodulationoftheDNAsubstrateaffectsHR(118,157),includingatspecicnuclearterri-toriessuchastelomeres(34)andthenucleolusHere,wereviewhowrecombinationalDNArepairisregulatedinmammaliansomaticandyeastvegetativecells.Weonlyincludeexam-plesofmeioticregulationofHRfactorsthatmayalsobeapplicabletosomaticcells.Thefocusisonthemechanisticphasesofrecom-bination(Figure1)andthefactorsthatexe-cutethem(Table1),identifyingkeyregulatorytransitionsandmechanisms.WeelaborateonhowHRismodulatedbymultiplelevelsofpos-itiveand,primarily,negativeregulation.Mech-anismsofantirecombinationappeartobeinte-graltotheHRpathway.WesuggestthatHRgainsexibilityandrobustnessbyproceedingthroughreversible,metastableintermediates.MECHANISMOFHOMOLOGOUSSignicantstrideshavebeenmadeinidentify-ingtheproteinsthatcatalyzeHRineukary-otesanddeningtheirmechanismsofaction(69,91,129,161).HRcanbeconceptuallydi-videdintothreestagespresynapsis,synapsis,postsynapsisandwebrieydiscusstheprinci-palproteinsandstructuresinvolved(Figure1114Heyer GE44CH06-HeyerARI3October201011:50 SDSAdHJ subpathway Noncrossover CrossoverNoncrossoverNoncrossover Half-crossover(LOH) Rad50-Mre11-Xrs2 Xrs2 Sae2 [CtIP],Exo1, Dna2 Sgs1-Top3-Rmi1,mi1,RPARad51, Rad52, Rad55-Rad57[RAD51B, RAD51C, RAD51D, XRCC2, XRCC3] BRCA2-DSS1Rad51, Rad54, Rdh54Sgs1-Top3-Rmi1 mi1 Mph1, Fml1 [FANCM]Slx1-Slx4, Yen1 [GEN1] Mus81-Mms4ms4Sgs1-Top3-Rmi1 mi1 Mph1, Fml1 [FANCM] Ku70-Ku80Pol4, ARTEMIS NHEJRad52, Saw1-Rad1-Rad10[ERCC1-XPF] Generic protein designationHuman-specic protein designationwith broken endsas repair template Synaptic phase Presynaptic phase Postsynaptic phase Homologous recombination (HR)D-loop Figure1 Pathwaysofdouble-strandbreakrepair.ProteinnamesrefertothebuddingyeastSaccharomycescerevisiae).Wheredifferentinhuman,names()aregiveninbrackets.Forproteinswithoutayeasthomolog,bracketsforhumanproteinsareomitted.BrokenlinesindicatenewDNAsynthesisandstretchesofheteroduplexDNAthatuponmismatchrepair(MMR)canleadtogeneconversion.Abbreviations:BIR,break-inducedreplication;dHJ,doubleHollidayjunction;NHEJ,non-homologousendjoining;LOH,lossofheterozygosity;SDSA,synthesis-dependentstrandannealing;SSA,single-strandannealing. MRX,MRN:SaccharomycescerevisiaecomplexorhumanNBS1complexproteinA Inpresynapsis,theDNAdamageispro-cessedtoformanextendedregionofsingle-strandedDNA(ssDNA),whichisboundbythessDNA-bindingproteinRPA(replicationpro-teinA).ForDNAdouble-strandbreaks(DSBs)inthebuddingyeastSaccharomycescerevisiaethisstepinvolvesasurprisingcomplexityoffournuclease[Mre11-Rad50-Xrs2(MRX)(humanMRE11-RAD50-NBS1[MRN]),Exo1,Dna2,Sae2(humanCtIP)]andahelicaseactivitySgs1(humanBLM;seesidebar)(104).Bind-ingofRPAeliminatessecondarystructuresinssDNA,whichisneededforcompetentRad51lamentstoassemble.However,RPAboundtossDNAalsoformsakineticbarrieragainstRad51lamentassembly,necessitatingso-calledmediatorproteinstoallowtimelyRad51lamentformationonRPA-coveredssDNA.Threedifferentclassesofmediatorshavebeendescribed,buttheirmechanismsRegulationofHomologousRecombination115 GE44CH06-HeyerARI3October201011:50 Table1PosttranslationalmodiÞcationsandtheireffectsonproteinsinvolvedinhomologousrecombination FunctionandPTMeffect Reference Homosapiens MultiplerolesinDNAdamagesignalingandHR BLM-K317/331-SUMOrequiredforfullactivityandRad51focusformationafterHUtreatment (47,120) H.sapiens E3ligaseinvolvedinHRandNHEJ PIAS1/4-dependentSUMOofBRCA1-K119enhancesBRCA1UBIligaseactivity H.sapiens RAD51lamentformation PO CDK-mediatedPOofS3291inhibitsRAD51interactionofC-terminalRAD51interactionsite H.sapiens DSBresection PO CDK-consensussiteT847requiredforCtIPactivity(seealsoSae2) CDK-consensussiteS237requiredforBRCA1bindingandHR Exo1 cerevisiae DNAexonuclease Rad53-mediatedPOofS372,567,587,692inhibitsExo1activity H.sapiens DNAexonuclease ATR-dependentPOleadstodegradation S.cerevisiae DNAligase4cofactor PO Dun1-dependentPOofNej1-S297/8enhancesbindingtoSrs2antirecombinasefavoringNHEJ/SSAoverHR S.cerevisiae Processivityclamp PCNA-K164(K127)-SUMOrecruitsSrs2antirecombinase (122,124) PCNA-K164-UBIpreventsSUMO,antirecombinationeffectbyfavoringTLSorforkregression (122,124) H.sapiens HomologysearchandDNA-strandinvasion CHK1-dep.POonT309mayberequiredforRAD51focusformation S.cerevisiae Rad51lamentformation,SSA SumoylationofK10,11,220affectsproteinstabilityandintranuclear (128,152) S.cerevisiae CofactorforRad51 Mek1-mediatedPOatT132inhibitsRad51interactionduringmeiosis mycespombe Co-factorforRad51 APC/CmediatedubiquitylationofRhp54-K26leadstoproteolysisinG1cells S.cerevisiae Rad51lamentassembly/stability PO Rad55-S2,8,14POrequiredforfullRad55activity S.cerevisiae DSBresection PO CDK-mediatedPOatS267requiredforSae2activity(seealsoCtIP) PTM,post-translationalmodication;PO,phosphorylation;UBI,ubiquitylation;SUMO,sumoylation.Theseresiduesrefertotherevisedstartcodonofatmethionine33(42)asdenotedinreference(128),whichcorrespondstoresidues43,44,210inreference(152).116Heyer GE44CH06-HeyerARI3October201011:50 DisplacementloopDNA-strandinvasionproductofthelamentleadingtothedifferentHRsubpathways(BIR,SDSA,dHJ)replication(BIR):asubpathwayofHRwhereasingle-endedDSBinvadesandestablishesafull-edgedreplicationHollidayjunctionjointmoleculeHRstrandannealingasubpathwayofHRwherethesecondendoftheDSBannealswiththeextendedstrandoftherstendDoubleHollidayjunction(dHJ):intermediateleadingtocrossovers.AlsousedheretolabeltheHRsubpathwaythatinvolvesthis ofactionandtheinterplaybetweenthemispoorlyunderstood.TheRad51paralogscon-stitutearstgroupandcomprisefourpro-teinsintwoseparatecomplexesinS.cerevisiae(Rad55-Rad57,Shu1-Psy3)andveinmam-mals(RAD51B,RAD51C,RAD51D,XRCC2,XRCC3).TheseproteinssharetheRecAcorewithRad51,butfailtoformextensivelamentsonDNAandareunabletoperformtherangeofDNA-pairingreactionscatalyzedbyRad51.AsecondclassistypiedbytheS.cerevisiaeprotein,whichperformstwoindependentroles:itsmediatorfunction,andasecond,laterfunc-tioninstrandannealingofRPA-boundssDNA.Athirdclassofmediatorproteins,apparentlyabsentinS.cerevisiae,isexempliedbyBRCA2,thehumanbreastandovariancancertumorsuppressorprotein.HumanBRCA2containsssDNAbindingmotifs(OB-folds),adouble-strandedDNA(dsDNA)bindingmotif(towerdomain),andanumberofRad51bindingsites,suggestingthatittargetsRAD51lamentnu-cleationtothedsDNAjunctionattheresectedend(168).Duringsynapsis,theRad51lamentper-formshomologysearchandDNA-strandinva-sion,generatingadisplacementloop(D-loop)withinwhichtheinvadingstrandprimesDNAsynthesis(Figure1).TheRad54motorproteinisrequiredforstabilizingtheRad51lamentandenhancingD-loopformationbyRad51,andforpromotingthetransitionfromDNA-strandinvasiontoDNAsynthesisbydissociat-ingRad51fromheteroduplexDNA(70).Finally,inpostsynapsis,thethreesubpath-waysofHRaredistinguished(Figure1),eachwithspecicenzymaticrequirementsthathavebeenonlypartiallydened(69,91,129,161).AsillustratedinFigure1,theD-looprepre-sentsthebranchingpointforthemultiplesub-pathwaysofHR(BIR,SDSA,dHJ).Intheab-senceofasecondend,theD-loopmaybecomeafull-edgedreplicationforkinaprocesstermedbreak-inducedreplication(BIR).Althoughthisprocessrestorestheintegrityofthechromo-some,itcanleadtoloss-of-heterozygosityofallgeneticinformationdistaltotheDSB.Inthepresenceofasecondend,thepredominantpathwayforDSBrepairinsomaticcellsap-pearstobesynthesis-dependentstrandanneal-ing(SDSA),inwhichtheextendedD-loopisreversed,leadingtoannealingofthenewlysyn-thesizedstrandwiththeresectedstrandofthesecondend(Figure1)(123).Thispathwayin-herentlyavoidscrossovers,whichreducesthepotentialforgenomicrearrangements.WhilegenerationofcrossoversbydoubleHollidayjunction(dHJ)formationisthepurposeofmei-oticrecombination,recombinationalDNAre-pairinsomaticcellsisrarelyassociatedwithcrossovers.OnlyrecentlyhavedHJsbeeniden-tiedasanintermediateinrecombinationalDNArepairinvegetative(somatic)cells(25).dHJformationinvolvescaptureofthesecondend,aprocessthatisactivelyblockedbytheRad51proteininvitro,suggestinganinher-entmechanisticbiastowardSDSA(167).ThedHJintermediatecouldberesolvedbyendonu-cleasesinamannerdescribedforthebacterialRuvCproteinintocrossoverornoncrossoverproducts(161),buttheexactmechanismsandidentityofproteinsinvolvedremainunderde-bate(seeFigure1).Alternatively,dHJscanbedissolvedbyacomplexmechanisminvolvingaRecQ-familyDNAmotorprotein(S.cerevisiaeSgs1orhumanBLM),topoisomerase3,andcofactors.Thetwojunctionsaremigratedto-wardeachother,leadingtoahemicatenanethatiseliminatedbyTopo3.Genetically,theendpointofdissolutionisalwaysanoncrossover,avoidingthepotentialforrearrangementsas-sociatedwithcrossovers(165).Crossoversaredenedasrecombinationeventsthatleadtotheexchangeofankingmarkers(Figure1)gen-eratingdeletions,inversions,ortranslocationswhennon-allelic,repeatedDNAsequencesareREGULATORYCONTROLPOINTSANDIRREVERSIBLEAnumberofreversibleposttranslationalmodicationsonHRproteins,suchasphosphorylation,ubiquitylation,andsumoy-lation,haverecentlybeenidentied(14,17)RegulationofHomologousRecombination117 GE44CH06-HeyerARI3October201011:50 dependentkinasestrandannealingamodeofhomology-directedDNArepairthatdoesnotinvolveDNA-strandinvasionbutdoesinvolveDNAnonhomologousend Table1).Someoftheseposttranslationalmodicationsmayleadtonovelproteininteractions,asindicatedbythepresenceofphospho-,ubiquitin-,andSUMO-specicpro-teininteractionmotifsinfactorsthatfunctionintheDDR,DNAreplication,DNArepairorHR(134).IrreversiblemodicationsincludeproteolyticcontrolofHRproteins(S.cerevisiaeSchizosaccharomycespombeTable1)(128,153)andexonucleolyticdegra-dationofDNAandendonucleolyticprocessingofDNAjunctionintermediates(Figure1SeveralkeyHRintermediates,suchastheRad51-ssDNAlament,theD-loop,andthedHJ,constitutereversibleintermediatesandhencelikelyregulatorycontrolpoints.Below,weprovideadetaileddiscussionofregulatorytargetsandprocesses,aswellastheirmechanis-ticconsequencesforHR.WhiletranscriptionalregulationisattheheartofthebacterialDNAdamageresponse(calledSOSresponse)(36),thereislittleevidenceofbiologicallysignicanttranscriptionalinductionofHRgenesbyDNAdamageineukaryotes(30,33,86).DOUBLE-STRANDBREAKREPAIR:COMPETITIONBETWEENHOMOLOGOUSSINGLE-STRANDANNEALING,ANDNONHOMOLOGOUSENDJOININGHR,single-strandannealing(SSA),andnon-homologousendjoining(NHEJ)aretheprin-cipalpathwaysforDSBrepair,andthebal-ancebetweenthemdependsonthespecies,celltype,cell-cyclestage,andtypeofDNAdam-age.NHEJisaspecializedligationreactionwithvaryingaccuracythatdependsontheendstructure(Figure1)(138).SSAisahomology-directedDNArepairpathwaythatpromotesrecombinationbetweentandemlyrepeatedDNAsequences,andinvolvesreannealingofRPA-coveredssDNAbytheRad52proteinFigure1)(91).SSAdoesnotinvolveDNA-strandinvasionandisthereforeindepen-dentofRad51.ThisprocessleadstodeletionoftheinterstitialDNAandoneoftherepeatedhomologoussequences.HowisthebalancebetweenNHEJ,SSA,andHRregulated?SSAandNHEJcanoc-curwithinthecontextofasingleDNAmolecule(Figure1),whereasHRisatemplate-dependentprocess,typicallyinvolvingtwoin-dependentDNAmolecules(sisterchromatids,chromosomes).StudiesinS.cerevisiaedemonstratedthatthesisterchromatidisthepreferredtemplateoverahomolog,whengiventhechoice(84).Sisterchromatidcohesionlikelyprovidesthemechanisticunderpinningforthispreference(111).ThiscouldsuggestthatHRisentirelyrestrictedtotheS-andG2phasesofthecellcyclewhenasisterchromatidispresent,butHRhasalsobeendemonstratedtooccurintheG1phaseofbuddingyeast,us-ingthehomologasatemplate(50).HRinG1canonlyoccurindiploidcells,andmostor-ganisms,includingS.cerevisiae,arenaturallydiploid.ThessionyeastS.pombe,ontheotherhand,isanaturallyhaploidorganism,preclud-ingrecombinationalDNArepairintheG1phase.ThisprovidesapossiblerationaleastowhyHRinssionyeastisdownregulatedintheG1phasebytargetingRhp54(ssionyeastRad54)forubiquitin-mediateddegradationInthebuddingyeastS.cerevisiae,themating-typelocusprovidesanexampleofcomplexregulationofHRinresponsetoploidy(156).Thediploid-specicMata1-Mat2corepres-sorturnsoffhaploid-specicgenesandinducesdiploid-specicgenes.OnegeneitregulatesisNej1,acofactorfortheprincipalNHEJlig-ase,DNAligase4,whichalsorecruitstheSrs2antirecombinase(seebelow)toresectedends.DownregulationofNej1thusshiftsthebalancefromNHEJorSSAtoHRindiploidcells(5,27,53,93).Thisalsoexplainsresultsofearlyradio-biologicalstudiesestablishingthata/cells,whichcontaintheMata1-Mat2core-pressor,aremoreradiation-resistantthanhap-loidcellsora/aordiploidcells,whichlackthisco-repressor(109).DSBresectionisakeycommitmentstepforhomology-directedrepairasbothSSAandHR118Heyer GE44CH06-HeyerARI3October201011:50 DNAdamagesynthesis(TLS):DNAsynthesisbyspecializedDNApolymerasesthatbypassesatemplatelesionwithoutrepairingitcellnuclearantigen dependonssDNA.Asdiscussedindetailbelow,DSBresectionishighlyregulatedandlowintheG1phase,favoringNHEJoverHRandSSA(54).Inbuddingandssionyeast,theNHEJDNAend-bindingfactorsKu70-Ku80inhibitDSBresection(92,151).Invertebratecells,theMRNcomplex,BRCA1,DNAPKcs,andATMfunctioninbothNHEJandHR(138).TheMRNcomplexandBRCA1areconnectedtoresection,providingapossibleregulatorytarget.Usingelegantsubstratedesign,itwasshownthatSSAandHRcompetefortherepairofDSBsinbuddingyeastandmammals(80,143).SinceSSArequiressufcientresectiontoexposedirectrepeatsasssDNA(Figure1),thebalanceisexpectedtobehighlylocusandassayHowIstheBalanceBetweentheSubpathwaysofHomologousRecombination(Break-InducedReplication,Synthesis-DependentStrandAnnealing,DoubleHollidayJunction)RegulatedDuringDouble-StrandBreakRepair?BIR,SDSA,andthedHJsubpathwaysofHRFigure1)leadtorepairofaDSBbutareasso-ciatedwithdifferentgeneticconsequences.BIRcanleadtoloss-of-heterozygositydistaltothebreaksite,whichcanhavedetrimentalconse-quencesifitcreatestwoidenticalallelesbear-ingadeleteriousmutation.dHJformationhasthepotentialtocreategenomicrearrangementsifHRoccursinnonallelicsites.SDSA,whichdoesnothavethesedeleteriousconsequences,isthefavoredsubpathway(123).ExperimentsinS.cerevisiaethattheSDSApathwayoutcompetesBIRinmitoticDSBrepair,becauseBIRisamuchslowerprocess(100).Usinganingeniousexperimentalsetup,Haberandcolleagues(81,145)demonstratedthatBIRissuppressedattheDNAsynthesisstepforovervehoursafterDSBformation.ThissuppressionrequiresSgs1,butsurprisinglynotitshelicaseactivity(81).Mec1kinase,themasterregulatoroftheDNAdamageresponse(DDR)inbuddingyeast(Figure3),isnotrequiredtosuppressBIR.CloseproximityofthesecondendsuppressesBIR(81),butitisunclearhowthisiscommunicatedtotheD-looptopreventreplicationforkassembly.Thismayinvolvetheend-tetheringfunctionoftheMRXcomplex(41).UnlikemeioticHR,dHJsareformedonlyatlowlevelsduringmitoticDSBrepair(25),consistentwiththelowassociationofmitoticDSBrepairwithacrossoveroutcome(78).DNAGAPREPAIR:COMPETITIONBETWEENTRANSLESIONSYNTHESIS,ANDFORKREGRESSIONReplicationforkstallingleadstogapsresultingfromdownstreamreinitiationbyDNApoly-merasesontheleadingandlaggingstrands(17,67,98).Stalledforksandgapscanberecov-eredbydifferentpathways,includingtransle-sionsynthesis(TLS),templateswitchingbyforkregression,orHR(17)(Figure2).Al-thoughtheaccuracyofTLSislesionandpoly-merasedependent(126),templateswitchingbyforkregressionandHRisinherentlyhighlyac-curate.TLSisfavoredbymono-ubiquitinationofproliferatingcellnuclearantigen(PCNA)onK164bytheRad6-Rad18E2-E3complexFigure2),whichenhancestheintrinsicafn-ityofY-familyTLSpolymerases(Poleta)forPCNAthroughtheirubiquitinbindingmotifs(126).InS.cerevisiae,subsequentpolyubiqui-tylationofPCNAbyUbc13-Mms2(E2)andRad5(E3)controlsforkregressionbyamech-anismthatisnotunderstood(126).Alterna-tively,K164(andK127)canbesumoylatedbyUbc9,whichleadstorecruitmentoftheSrs2antirecombinasethroughitsSUMObindingmotif(122,124).Asdiscussedinmoredetailbelow,Srs2dissociatesRad51fromssDNA,an-tagonizingRad51-ssDNAlamentformation(90,158).ItisunclearwhetherPCNAubiq-uitylationandsumoylationcancoexistinahetero-trimericPCNAring,andtherelation-shipbetweenHRandtheseubiquitylationandRegulationofHomologousRecombination119 GE44CH06-HeyerARI3October201011:50 ork incision ap repair Stalled fork Repair recombination E2: Rad6E3: Rad18Rad55 - Poly-UbMono-Ub E2: Mms2Ubc13E3: Rad5 RAD51- CDKDDR ??K164K Gap invasion End invasion TranslesionsynthesisForkregression Figure2 Pathwaysandregulationatstalledreplicationforks.Proliferatingcellnuclearantigen(PCNA)modicationregulatesthechoiceofcompetingpathwaysforstalledreplicationforkrecovery.AstalledforktriggerstheDNAdamageresponse(DDR),whichdirectlyactivateshomologousrecombination(HR).TherelationshipbetweentheDDRandcell-cyclecontroltoPCNAsumoylation/ubiquitylationhasnotyetbeendetermined.sumoylationpathways(Figure2)isstillpoorlyunderstood(18,19).HowisthebalancebetweenTLS,forkre-gression,andHRregulated?GeneticevidenceinbuddingyeastfavorsthemodelthatTLSandforkregressionareprimarypathways.Atleastinitially,HRisactivelyrepressed,butthesensi-tivityofHRmutantstoforkstallingagentssug-geststhatthisinhibitionistemporary.Muta-tionsindisableTLSandforkregression,leadingtosevereDNAdamagesen-sitivity.Anadditionalmutationinpressorofradsix)suppressesthesensitivitytoasignicantdegreebyrelievingtheinhibitionofHR(2,132).ThesedatasuggestthatRad6-Rad18bindingtoRPA-coveredssDNA(39)iskineticallyfavoredoverRad51lamentforma-tion.Possibly,PCNAsumoylationmarksalaterphasewhereSrs2activelyremovesRad51l-aments.WhatregulatesPCNAubiquitylationorsumoylationandwhetherDDRsignalingisinvolvedremaintobedetermined.SIGNALINGBYTHECELL-CYCLEMACHINERYANDTHEDNADAMAGERESPONSETwosignalingsystemsintersectinthecontrolofHR:thecell-cyclecontrolmachineryandtheDDR(Figure3)(17).InS.cerevisiae,theCdc28CDKdrivesdirectionalprogressthroughthecellcycle,dependentontheexpressionof120Heyer GE44CH06-HeyerARI3October201011:50 Cell cycle Majorevents inchromosome CDK-cyclin(S. cerevisiae)CDK-Cln1, Cln2, Cln3CDKÐClb5, Clb6CDKÐClb1, Clb2, NHEJ versus HRNHEJ NHEJ NHEJ CDK regulation of DSB repair phosphorylationstate(vertebrates) KU70 phosphorylationstate 3'5'3'5'3'5' processing DDR signaling and DNA repairATRResectionATRIP Cdc25 Cell cycleforkRad55FANC 3' RPAATM P P P P HR most active HR least active Figure3 recombination(HR)isregulatedbycell-cyclecontrolandDNAdamagesignaling.)Thecellcyclecontrolsthecompetitionbetweennonhomologousendjoining(NHEJ)andHRindouble-strandbreak(DSB)repair.Cdc28isthesolekinase(CDK)responsibleforcell-cycleprogressioninSaccharomycescerevisiaeandpartnerswiththeindicatedcyclins.Inmammals,sixCDKsdrivecell-cycleprogression,andtheirrelativeimportancevariesindifferenttissuetypes.()TheDNAdamageresponse(DDR)resultsinHRactivationandinhibitionofcell-cycleprogression.TherelationshipbetweentheDDRandtheFanconianemia(FANC)pathwayaswellasproliferatingcellnuclearantigen(PCNA)sumoylation/ubiquitylationispoorlyunderstood.Abbreviations:NHEJ,non-homologousendjoining;HR,RegulationofHomologousRecombination121 GE44CH06-HeyerARI3October201011:50 ionizingradiation stage-speciccyclinsthatmodulateCDKactivityandimpartsubstratespecicity(101,163).Asdiscussedbelow,CDKphosphorylatesHRproteinstopositivelyandnegativelyreg-ulateHR.TheavailabilityofsisterchromatidslargelydetermineswhetherHRisaprimarypathway,explainingwhyHRisfavoredintheSandG2phasesbutnotintheG0,G1,orMphases(Figure3).StalledreplicationforksandDNAdamagetriggertheDDRsignalingcascadethatactivatesDNArepairandpausescell-cyclemomentum(Figure3)(17).ThekeyintermediateisRPA-boundssDNA,whichservesasaplatformforDDRsignaling,recruit-mentofubiquitylationand,likely,sumoylationfactors,aswellasforRad51lamentformation.DDRsignalingisrequiredforefcientDNAdamageinducedHR(13,108,141).Inaddi-tion,theDDRaffordstimeforHRtobecom-pletedbyleadingtoatransientcell-cyclearrest,whichinmostorganisms,butnotS.cerevisiaeisachievedbydownregulatingCDKactivityDOUBLE-STRANDBREAKRESECTIONANDITSResectionofDSBendsseemsdeceptivelystraightforwardinprinciple,butinS.cerevisiaeresectioninvolvesfournucleases(Mre11,Sae2,Exo1,Dna2),dependentonthespecicchem-icalstructureencounteredattheDSB(hair-pins,modiedbases,covalentproteinDNAadducts)(104).AcurrentviewproposesthattheMre11subunitoftheMRXcomplex,re-cruitedorsupportedbytheendonucleaseSae2,catalyzesinitialendprocessingthatresultsintheremovalofabout50100nucleotides(104).Sae2isthoughttoclipDNAendsinprepa-rationforthemoreprocessivenucleasesthatcatalyzetheextendedresectionresponsiblefor-ssDNAtailgeneration(94).The3larityoftheMre11nucleaseappearsunsuitedtoconductthe5resection(154),butitcouldactasanendonucleaseinthiscontext.Extendedresectionisachievedbythe5aseactivityofExo1orthehelicaseactivityofSgs1incooperationwiththeendonucleaseac-tivityofDna2(103,174).HowtheseoptionsforextendedDNAresection(Exo1aloneorSgs1withDna2orExo1)ortheextentofresectionareregulatedisunknown.Compoundingthecomplexityassociatedwiththecollaborationofmultiplenucleasestoachieveendresectionisthequestionoftheirregulationbyposttransla-tionmodication.ActivationofDSBResectionbyCDK-MediatedSae2/CtIPInhaploidS.cerevisiaecells,limitedendre-sectioncanrestrictrepairofaDSBbyHRintheG1phaseofthecellcycle(7,79).Inyeast,endresectionisprimarilyregulatedbyCDK-dependentphosphorylationoftheSae2nuclease(74,79)(Figure3Table1),whichdetermineswhetheraDSBischanneledintoNHEJorHR.Thepivotalphosphorylationoc-cursatserine267,locatedinoneofthreeSae2CDKconsensussites(74).Anendonuclease-mediatedDSBatthelocusispoorlyre-sectedinanS.cerevisiaesae2-mutant;amutantinwhichserine267hasbeensubsti-tutedwithalanine()phenocopiesstrainforunresectedDSBends.Incontrast,aSae2phosphomimicmutantinwhichserine267hasbeenreplacedwithaspar-ticacid()ishypermorphicforDSBresection,sidesteppingarequirementforCDKactivitytosanctionDSBresection.Theseobservationsaremirroredbyresultsfromhumancells,whereCtIP,thehumanho-mologofSae2,isalsorequiredforDSBresec-tion(130).Phosphorylationonthreonine847isrequiredforssDNAgenerationandRPAphosphorylationinresponsetothetopoiso-meraseIinhibitorcamptothecin,laser-inducedDNAdamage,orionizingradiation(IR)(75).AtransfectedphosphomimicCtIP-T847Ere-sectsDSBsevenafterCDKinhibition,whereasthenonphosphorylatableCtIP-T847Amutantimpairsresection(75).CDKphosphorylationofSae2/CtIPthereforeappearstobeconservedineukaryotesasakeyswitchindetermining122Heyer GE44CH06-HeyerARI3October201011:50 whetherDSBendsaresanctionedforresectionandHR.Inadditiontotheconservedmech-anismdescribedforS.cerevisiaeSae2,humanCtIPfunctionalsoappearstoberegulatedbyanadditionalCDKphosphorylationatserine327,amodicationthatenhancesCtIPinter-actionwiththeBRCTdomainofBRCA1andiscriticalforHR(171,173).ThefunctionofBRCA1inHRremainsenigmatic.Itisinter-estingtoobservethatBRCA1issumoylatedbyPIAS1/4toenhanceitsubiquitinligaseactivityTable1)(57,107)andthatCtIPappearstobeoneofitsnativeubiquitylationtargets(172),implyingapotentialregulatoryroleofBRCA1inresection.Sae2-S267inS.cerevisiaeisunlikelytobetheexclusivetargetofCDKrelevanttoendresec-tion,becausethemimicmutationdoesnotcompletelyrestoreresectiontowild-typelevels(74).AlthoughMre11andXrs2haveCDKphosphorylationconsensussites,noresectionphenotypehasbeenobservedwhenthesesitesaremutated(79).Thus,additionaltargetsremaintobeAsecondsignalingpathway,whichdependsoncell-cyclecontrols,alsoregulatesSae2,asMec1/Tel1consensussites,whichareessentialformeioticrecombination(26,150),arealsore-quiredforfullSae2functionduringDNArepairinmitoticcells(12).Insummary,twosignalingpathways,thecell-cyclecontrolmachineryandDDRsignaling,convergeonSae2/CtIPtoreg-ulateendresection.InhibitionofExo1ActivitybytheDDRKinaseRad53Exo1isoneofthenucleasesthatgeneratesthessDNAthatisadeningintermediateofDSBprocessinginHR.ssDNAalsooccursattelom-eresthatareuncappedduringend-replicationinSphaseandinmutants(e.g.,)thatlosetheprotectiveT-loopandassociatedfac-tors(34).FourserinesintheS.cerevisiaeExo1C-terminusaretargetsforregulatoryphosphorylation,presumablybyRad53,be-causeExo1phosphorylationisabsentinakinase-defectivemutant(106).OverexpressionofExo1resultsinhyperactiva-tionoftheDDR,consistentwiththegenera-tionofexcessssDNA.Thesamephenotypeisobservedinmutantsinwhichallfourserinesaresubstitutedbyalanine,suggestingthatRad53-dependentphosphorylationreducesExo1ac-tivity.UnlikeSae2/CtIPactivationbyCDK,Exo1phosphorylationlimitsresectionofssDNAatuncappedtelomeresandconse-quentlyminimizesfurtheractivationoftheDDR.TheinhibitionofExo1activityisnotlimitedtopathologicalsituationssuchastelom-ereuncapping.Exo1isalsophosphorylatedmutantcellsfollowingbleomycintreatment(106).RepressionofExo1activitybyDDRsignalingislikelyinvolvedintheavoid-anceofforkregressionatstalledreplicationforks(Figure2)(35).AnothermechanismofnegativeregulationofEXO1isobservedinhu-mancellschallengedwiththereplicationin-hibitorhydroxyurea(HU),wherephosphory-lationbyATRtargetsEXO1fordestruction(48).ThismayreectaprohibitionofresectionatssDNAgapsassociatedwithstalledreplica-tionforks.TheseresultssuggestthatExo1isnotrequiredforthegenerationofssDNAtoallowDDRsignalingandthatforkregressionandpotentiallyHRmayrequiremoreextensivestretchesofssDNAgeneratedbyExo1.RegulationofHumanBLMHelicasebySumoylationBiochemicalandgeneticevidencedemonstrateaninvolvementoftheRecQhelicasesSgs1(yeast)andBLM(human)inDSBresection(62,103,114,174)besidesfunctionsinjointreversal,dHJdissolution,andDDRsignaling(15).SumoylationofBLMmayexertpositiveregulation,asBLMisnormallysumoylatedonseverallysineresidues,andBLMlack-ingsumoylationonlysineK317andK331Table1)onlypartlycomplementedthege-neticdefectsinBLM-decientcells(47).TheobservationthatcellswithSUMO-decientBLMexhibitadefectinRAD51focusforma-tionafterHUtreatment(120)maysuggestRegulationofHomologousRecombination123 GE44CH06-HeyerARI3October201011:50 thatsumoylationisrequiredforaprorecom-binationactivityofBLM,possiblyresection(48,106).Insummary,posttranslationalmodica-tionoffactorsinvolvedinDSBresectionisparamounttotheregulationofeukaryoticHR.Tworegulatorypathways,cellcyclecontrolandtheDDR,exertpositiveandnegativecontrol,respectively,directlyphosphorylatingtwonucleases(Sae2/CtIPandExo1).CDK-dependentmodicationofyeastSae2/humanCtIPdemonstratesthatpathwaychoiceforDSBrepairdependstoalargeextentoncom-mitmenttoresection.THERAD51FILAMENT:ABALANCEBETWEENFORMATIONANDDISRUPTIONTheRad51-ssDNAlamentperformsthecen-tralfunctions:homologysearch,andDNA-strandexchange(Figure1).Notsurprisingly,thiscrucialroleisreectedinanelaboratereg-ulationofthebalancebetweenRad51lamentformationanddisruption.CDK-andDDR-MediatedPhosphorylationofRPARPAfunctionsatthenexusofallDNAmetabolicprocessesbecauseofitshighafn-ityforssDNA.RPA-coveredssDNAisthephysiologicaltargetforassemblyoftheRad51-ssDNAlament.Rad51lamentformationcompeteswithotherprocessesthatoccuronRPA-coveredssDNAsuchasrecruitmentoftheRad6-Rad18ubiquitylationcomplex,TLS,forkregression(Figure2),andATRsig-naling(Figure3).RPA2,themiddlesub-unitofRPA,undergoescellcycledependentandDNAdamageinducedphosphorylationinyeastandhumancells(52).RPAphospho-rylationdoesnotappeartoaffectitsDNAbindingproperties,butlikelymodulatespro-teininteractionsthatmayaffectitsintranuclearlocalization(52).PositiveControlbyDDR-MediatedRad51PhosphorylationInresponsetoHU,humanRAD51isphospho-rylatedbyCHK1kinasewithinaconsensussiteatthreonine309(Figure2Table1)(141).CellsdepletedforCHK1activitybyUCN-01-mediatedinhibitionorsiRNAdisplayadefectinRAD51focusformationinresponsetoHU,whichisconsistentwithpositiveregulationofHRbyCHK1.TargetsotherthanRAD51maybeinvolvedaswell.ExpressionoftheRAD51-T309Aphosphorylation-defectivemutant,butnotthewild-typeprotein,causesdominanthy-persensitivitytoHU,supportinganactivatingroleofthreonine309phosphorylation(141).NegativeControlbyCDKPhosphorylationofBRCA2ThetumorsuppressorproteinBRCA2(seesidebar)playsakeyroleintheformationoftheRAD51lament(129).CDK-cyclinAcanphosphorylateBRCA2onserine3291invitro,andthisresidueisalsophosphorylatedinvivo,peakingduringMphase(Figure2Table1(49).S3291ofBRCA2isneartheC-terminalRAD51interactionsite(residues31963226)(135),andphosphorylationofthisresidueormutationofserinetoalanineablatestheinter-actionoftheBRCA2C-terminuswithRAD51(49).ThesedataledtothemodelthatCDK-mediatedBRCA2phosphorylationprecludesHRduringMphase,whereitcouldinter-ferewithchromosomesegregation(49).Fur-thermore,BRCA2andtheRAD51paralog,RAD51C,arealsoinvolvedinnucleartransportofRAD51afterDNAdamage(40,61).Rad52SumoylationAffectsProteinStabilityandIntranuclearLocalizationRad52isthelynchpinofHRinS.cerevisiaeisessentialbothforHRandSSA(69,91,129,161).SumoylationofasignicantfractionofyeastRad52proteinisinducedinmeiosisoraf-terDNAdamage,dependentontheMRXcom-plex(128).Atriplemutantatlysineresidues124Heyer GE44CH06-HeyerARI3October201011:50 sisterchromatid 10,11,and220ablatedRad52sumoylation,leadingtofasterproteasome-dependentpro-teinturnover(128)(Table1).WhileSUMO-decientRad52proteinislargelyprocientforHR,themutantdisplayeda2.5-foldreductionindirectrepeatrecombination(128).Livecellimagingrevealedthatsumoylationcontrolsnu-cleolarlocalizationoftheRad52protein.Inwild-typecells,Rad52proteinisexcludedfromthenucleolus,thenuclearcompartmentcon-tainingtherDNArepeats.TheRad52SUMO-decientmutantovercomesthenucleolarex-clusionandformsfociwithinthenucleolus,re-sultinginslightlyelevatedrDNArecombina-tion(152),oppositetotheeffectonnuclearre-peatrecombination(128).PhosphorylationofRad55Serines2,8,and14IsRequiredforOptimalHRInyeast,theRad51paralogcomplexconsist-ingofRad55andRad57facilitatestheforma-tionorstabilizationofRad51laments(97,147).Rad55isphosphorylatedinresponsetoDNAdamageonmultipleresiduesbyMec1(serine378),Rad53(serine14),andanuniden-tiedkinase(serines2and8)(13,68,82).TheN-terminalphosphorylationmutant(Rad55-S2,8,14A)displaysstrongdefectsingrowthandsurvivalinresponsetothealkylatingagentmethylmethanesulfonate.Theseconditionsleadtoreplicationforkstalling,andRad55phospho-decientmutantsexhibitadefectintherecoveryofstalledreplicationforks(68)Table1DisruptionofRad51-ssDNAFilamentsbyAntirecombinogenicDNAHelicasesTheyeasthelicaseSrs2istheprototypeforan-tirecombinationhelicasescapableofdisruptingRad51-ssDNAlaments(90,158)(Figure2exertingbiologicallysignicantantirecombina-tionactivity(1,29,132).DuringS-phase,Srs2isrecruitedtoreplicationforksbysumoylatedPCNA(Table1)(122,124).Similarly,theyeastNHEJfactorNej1recruitsSrs2toDSBstorepressHRandfavorNHEJorSSA,andthisin-teractionisenhancedbyDNAdamageinducedphosphorylationofNej1byDun1kinaseTable1)(27).Srs2hasnodirectorthologinmammals,butgeneticstudieswithhumanFBH1inbuddingyeasthaveledtotheproposalthatFBH1isthemammaliancounterpartofyeastSrs2(32).Thisisconsistentwiththeorig-inalidenticationofFbh1asasuppressorofahypomorphicmutantintheS.pomberad22(homologofS.cerevisiaeRAD52)(119).More-over,overexpressionofhumanFBH1inhumancellsimpairedrecruitmentofhumanRAD51tossDNAandsuppressedHR,whereasFBH1depletioncausedanincreaseinsisterchromatidexchanges(SCEs)(56),whichisconsistentwithanantirecombinationroleofFBH1.RECQ5,aRecQfamilyhelicaseinmam-mals(seesidebar),mayplayanantirecombino-genicrole(15).ItinteractswithRAD51anddis-placesRAD51fromssDNAtoinhibitD-loopformationinvitro(73).Inaddition,adefectinRECQ5causesincreasedlevelsofspontaneousRAD51foci,aswellaselevatedfrequenciesofspontaneousDSBsandHRbetweendirectre-peats(73).BLM,anothermammalianRecQfamilymember(seesidebar),alsointeractswithRAD51andiscapableofdisruptingRAD51-ssDNAlamentsinvitro(23,166).Thebio-logicalrelevanceofthisobservationisuncer-tainbecauseBLMonlydisruptslamentsinconditionscontainingMg,whichhasbeeninterpretedastargetingtheADP-bound,inac-tiveformofRAD51anddoesnotdissociatetheATP-boundRAD51inthepresenceofCa(22,23).FANCJ,acomponentoftheFanconiAne-miapathway(seesidebar)(105),exhibitsa5directionality,incontrasttotheRecQfam-ilyhelicases.AswithBLM,humanFANCJdis-ruptsRAD51-ssDNAlamentsinvitrobutdis-sociatesonlytheinactive,ADP-boundformofRAD51fromssDNAinvitro(140).Nospe-cicinteractionbetweenFANCJandRAD51hasbeenreported.ThebiologicalsignicanceofRAD51dissociationbyFANCJremainsun-clear,asamutantin,theRegulationofHomologousRecombination125 GE44CH06-HeyerARI3October201011:50 Caenorhabditiselegans,showsnosignicantincreaseinRad51foci(169).Insummary,theRad51-ssDNAlamentiscontrolledbyabalancebetweenmedia-torproteinsthatpromoteassemblyandan-tirecombinogenicDNAhelicasesthatpromotedisassembly.CellcycledependentandDNAdamageinducibleposttranslationalmodica-tionsofthesefactorsimpingeonbothassemblyanddisassemblyoftheRad51lament.REGULATIONOFHOMOLOGYSEARCHANDDNA-STRANDHomologysearchandDNA-strandinvasiongenerateD-loops,akeyintermediateforallsubpathwaysofHR(Figure1).Thesereac-tionsarecatalyzedbyRad51,whichinteractswiththedsDNAmotorproteinRad54(70).Inmeiosis,acriticalproteininteraction(Rad51-Rad54)istargetedtoassertnegativeregulationofHRbyMek1-mediatedphosphorylationofRad54-T132(115)(Table1).ThismechanismisindependentofHed1(115),ameiosis-specicrepressoroftheRad51-Rad54interactionthatbindstoRad51protein(24,155).Bothmecha-nismsareactiveinmitoticcellswhenHed1ortheRad54-T132Dphosphomimicmutantareectopicallyexpressed(24,115,155).REVERSIONOFD-LOOPSANDEXTENDEDD-LOOPS:PRO-ANDANTIRECOMBINOGENICDisruptionofaD-looppriortoextensionoftheprimerstrandbyDNApolymerasesisapoten-tiallypowerfulmechanismofantirecombina-tion.AnumberofDNAhelicases/translocases,includinghumanFANCM,itsS.cerevisiaemologMph1andS.pombehomologFml1,metazoanRTEL1,mammalianRECQ1andBLM,aswellasRad54,arecapableofdis-ruptingD-loopsinvitro(Figure4)(8,11,20,21,59,146).However,reversionofanex-tendedD-loopisalsoinherenttotheSDSApathwayandconstitutesinthiscontextaprore-combinationactivity(Figure1).Insomege-neticassayssuchanactivitycanbescoredtosuppresscrossovers,constitutingamechanismofanticrossoverotherthandHJdissolutionFigure1Rad54isessentialforHRinbuddingyeastandisrequiredforinvitroD-loopforma-tionbytheyeastRad51protein(70).However,Rad54canalsodissociateD-loopsinvitro(21),theveryproductitformsinconjunctionwithRad51,makingitdifculttotestthebiologicalsignicanceofthisactivity.Inyeast,geneticstudiesonSgs1havepro-videdcriticalinsightsonthecellularfunctionsandregulationoftherelatedhumanRecQhe-licasesinHR(15).However,themultiplefunc-tionsofSgs1inDDRsignaling,DSBresection,dHJdissolution,andpotentiallyotherstepsofHRcomplicateinterpretationofthegeneticdata.Importantly,Sgs1suppressescrossoversduringmitoticandmeioticrecombination(78,117).ThisroleofSgs1correlateswiththeabilityofthehumanBLM-TOPO3alpha-RMIcomplextodissolvedHJsintononcrossoverproducts(165).dHJdissolutionbyhumanBLMhelicasealsoexplainstheelevatedlevelsofSCEinBLM-decientcells(seesidebar).BLMmayalsocontributetoanoncrossoveroutcomebypromotingtheSDSApathway,asindicatedbygeneticstudiesin(3).HumanBLMinteractswithhumanRAD51proteinandcandissociatemobileD-loops(8,166),butnotD-loopsduringanongoingRAD51-mediatedinvitroreaction(114).Thisleavesopentheques-tionofhowBLMmaypromoteSDSA.HumanFANCMproteinisacorecom-ponentintheFanconiAnemiapathwaythatiscriticalfortherepairofinterstrandDNAcrosslinks(105).FANCManditshomologsformanevolutionarilydeeplyrootedfamilythatincludesthearchaealHefnuclease/helicase,buddingyeastMph1,andssionyeastFml1.Theeukaryoticenzymeseitherlostordegen-eratedtheirnucleasedomain(162).FANCM-decientcellsdisplayelevatedlevelsofspon-taneousSCE,consistentwiththeabilityofFANCMproteintodissociatemobileD-loops(9,59,127).TheFANCpathwayis126Heyer GE44CH06-HeyerARI3October201011:50 Rad54RPARad51 Rad51-dsDNAdead end complex Rad51, Rad54, Rdh54Rad54DNA PolRad52Rad55Rad57d57BRCA2-DSS1Srs2, FBH1BLM, RECQ5 FANCJMph1, RTEL1Fml1 [FANCM] [BLM, RECQ1] Crossover/noncrossoverNoncrossoverSlx1Slx4, Yen1[GEN1]Mus81Mms4 ms4 Rad51-ssDNAlamentD-loopExtendedD-loop Sgs1-Top3-Rmi1[BLM-TOPO3 Forward pathways Reverse pathways RPA Rad51Generic protein designationHuman-specic protein designation Figure4 Reversible,metastableintermediatesinhomologousrecombination(HR).HRisproposedtoinvolvekeyintermediatesthatarereversibleandmetastableincluding()theRad51-ssDNAlament,()theinitialD-loop,()theextendedD-loop,and()thedoubleHollidayjunction(dHJ).Thedead-endcomplexofRad51/Dmc1withdsDNA,althoughnotanHRintermediate,canbeaddedtothislistofreversibleHRproteinDNAcomplexes(72).negativelyregulatedinmitosisbypolo-likeki-nasePLK1phosphorylationofFANCM,lead-ingtoitsubiquitin-mediateddegradation(88).SimilartohumanFANCM,Mph1andFml1dissociateD-loopsinvitro(125,146).Ade-fectintheyeastFANCMorthologs,Mph1orFml1,alsocausesathree-tofourfoldincreaseincrossovers.EpistasisanalysisinbothssionandbuddingyeastsuggeststhatMph1andFml1actindependentlyofSrs2orSgs1insuppress-ingcrossovers(10,125,146).BothproteinspromoteRad51-dependentrecombinationatstalledreplicationforks(121,133,146).Us-inganinduciblereplicationforkstallingsystemRegulationofHomologousRecombination127 GE44CH06-HeyerARI3October201011:50 betweensimilarbutnotidenticalsequences,asfoundinrepeatedDNA inssionyeast,Whitbyandcolleagues(146)showedarequirementforFml1inspontaneousandforkstallinginducedHR.Moreover,inS.cerevisiae,mutantsinhavethesamemutatorphenotypeasHRmutants(andthiseffectisepistaticwithanHRde-fect,suggestingthatMph1functionsinconcertwithHRtoavoidRev3-dependentmutagene-sis(133).Mph1appearstofunctionlateinHR,asthesyntheticlethalitywithissuppressedbymutationsinrad51,rad55,rad57,(133).However,Mph1hasalsobeensuggestedtopromotegrosschromosomalrearrangementsbyinhibitingHRthroughstabilizingRPAonssDNA(10).RECQ1,anothermammalianRecQfamilyhelicase,isrequiredforgenomestabilityinmouseandhumancells,asRECQ1deciencyleadstoaneuploidy,chromosomalinstability,andhypersensitivitytoDNAdamage(IR,camptothecin)(136,137).RECQ1-decientcellsexhibitincreasedlevelsofspontaneousDNAdamageassuggestedbyanincreaseinspontaneousgamma-H2AXfociandelevatedSCElevels.Invitro,RECQ1disruptsD-loops,withsignicantpreferenceforD-loopsresult-ingfrominvasionofthe5-end(20).GiventhatDNApolymerasecannotextendsuchaD-loop,itconstitutesapotentialdead-endcomplex.ThisactivityprovidesaplausiblemechanismforRecQ1functioninreversingapotentiallytoxicHRintermediate.TheRAD3-likehelicaseRTEL1wasiso-latedinascreenforfunctionalanalogsofSrs2C.elegans(11).Adefectincausessyn-theticlethalitywhencombinedwithmutationsaswellasafour-foldincreaseinmeioticcrossoversandDNAdamagesensitivitytointerstrandcrosslinksandthetopoisomeraseIinhibitorcamptothecin(11,170).DepletionofRTEL1inhumancellscausesafourfoldincreaseinDSB-mediatedin-trachromosomalrepeatrecombinationthatisimprobablyexplainedbyadefectincrossoversuppression,aswellashypersensitivitytothecrosslinkingagentmitomycinCbutnotIR(11).Invitro,RTEL1dissociatesD-loops,whichcouldexplaintheantirecombinationandanticrossoverphenotype(11,170).TheDNAdamagesensitivityproleofmutantsismoreconsistentwithadefectinHR,suggestingthatRTEL1mayplayaroleinSDSA(170).InC.elegans,mutationsinshowasyn-theticphenotypewithadefectintheHELQ-1DNAhelicase,leadingtoaccumulationofHRintermediatesinthedoublemutantasdeducedfromthepersistenceofmeioticRAD-51foci(159).UnlikeyeastSrs2,RTEL1cannotdis-sociateRAD51fromssDNA(11,90,158).In-terestingly,Iraetal.(78)postulatedthatSrs2exertsitsanticrossovereffectthroughafunc-tioninSDSAandsuggestedthatSrs2disso-ciatesD-loops.However,thisbiochemicalac-tivityhasnotbeenobservedinvitro(90,158).ThestimulationofSrs2helicaseactivitybyRad51boundtodsDNAsuggeststhepossibilitythatSrs2targetstwoHRintermediates,Rad51-ssDNAlamentsand(extended?)D-loopsInsummary,anumberofproteinsarecapa-bleofdissociatingD-loops,whichmayfunctioninHRtofavorSDSAandsuppresscrossoversormaybeamechanismofantirecombination.Themutantphenotypessuggestpotentiallycom-plexrolesinvolvingpro-andantirecombinationfunctionsforRTEL1,Srs2,Sgs1/BLM,andtheFANCMhelicasesinHR.MISMATCHREPAIREDITSRECOMBINATIONFIDELITYMismatchrepair(MMR)editsreplicationer-rors,andmismatchcorrectioninheteroduplexDNAachievesgeneconversionduringHRFigure1).MorecriticaltotheregulationofHR,however,isthatMMRproteinshelptodiscriminatehomologyfromhomeology(partialhomology)(65).ThisMMR-mediatedscreeningofrecombinationdelityfavorsHRbetweenperfectlyhomologoussequencesandactivelyopposeshomeologousrecombination,respondingtothedegreeofhomology.GeneticstudiesinS.cerevisiaecallysurveyedtheeffectsofhomeologyonHRusinganelegantintron-basedassay(37,38).Remarkably,evenasinglemismatchreduced128Heyer GE44CH06-HeyerARI3October201011:50 describesoutcomeofHRwithrespecttotheankingDNA,whichiseitherinparental(noncrossover)or spontaneousrecombinationratesbyfourfoldrelativetosubstrateswith100%identity.Mostimportantly,defectsinMMRsuppressedtheeffectsonspontaneousHRrateswhenhomeol-ogywasupto15%sequencedivergence.MMRfactorsthereforeregulatewhetherHRissanc-tionedovergivensequenceswhentheinter-actingsequencesare85100%similar.Threeyeastcomplexesfunctioninbothreplication-associatedMMRandinnegativeregulationofHR:MutS(Msh2-Msh6),MutSMsh3),andMutL(Mlh1-Pms1)(37,38).Inaddition,thenucleasesRad1-Rad10andExo1,andthehelicasesSgs1andSrs2functionintheMMR-mediatedbarriertoHRbetweenhomeologoussequences(113,160).MMRnotonlyaffectsthefrequencyofHRbutalsoin-uencesthecrossover/noncrossoveroutcomeofHR(Figure1)(160).ThischaracteristicoftheMMR-mediatededitingofHRmaybepar-ticularlyusefultosuppresscrossoversbetweenslightlydivergentrepeatedDNAsequences,wherecrossoverswouldleadtogenomeWhatisthemechanismoftheMMR-mediatedbarriertoHRbetweendivergentsequences?SuppressionofhomeologousrecombinationbyMMRcouldfunctionduringDNA-strandexchange,heteroduplexDNAextension,orevenlater,injointmoleculeres-olution(Figure1).ParadigmaticbiochemicalstudieswithbacterialRecA,MutS,andMutLproteinssuggestthatheteroduplexDNAex-tensionmaybethedecisivestage(164).Similarbiochemicalworkwitheukaryoticproteinshasnotbeenreported,butgeneticevidencefromS.cerevisiaeisconsistentwiththisscenario.Mi-toticandmeioticgeneconversiontractsinmutantsare50%longerthaninwild-typecells,indicatingthatheteroduplexDNAextensionmaybeblockedbyMsh2-Msh3bind-ingtomismatchesinvivo(31).S.cerevisiaeandMph1arecandidatesformotorproteinsac-tiveinheteroduplexDNArejection(110,149).mutantsallowedanincreasedrateofhome-ologousHR(substratewith91%sequenceidentity),synergisticwithMMRmutants(142).ThisincreaseinhomeologousrecombinationwasalsolinkedtoaroleforSgs1insuppressionofgrosschromosomaltranslocations(110).Inaddition,Sgs1andMsh2-Msh6suppressSSAbetweenhomeologoussequences(144).Insummary,MMRisakeyregulatorofHRinthedistinctionbetweenallelicsitesandec-topicsites.Thiseditingfunctionissufcientlysensitivetodiscriminateallelictargetsonsisterchromatidsfromallelictargetsonhomologs.TheimportanceofMMRinfocusingHRtoperfectsequenceidentity(allelicsitesonsisterchromatids)suggeststhatMMRdefectsintu-morsnotonlyincreasetheratesofpointmu-tations,butalsoincreaseratesofinappropriateHRbetweenhomeologoussequencesleadingtogenomerearrangements.NUCLEOLYTICPROCESSINGOFSTALLEDREPLICATIONFORKSANDDOUBLEHOLLIDAYAnumberofDNAjointmoleculesareinter-mediatesatwhichregulatorydecisionscanbemade,providingsuccessiveopportunitiestode-cidewhetherHRisinitiated,aborted,orsanc-tionedforaspecicgeneticoutcome(crossoverornoncrossover).TheregulationofHRrele-vanttotwospecicjointmolecules,replicationforksanddHJs,iselaboratedhere.Stalledreplicationforksarepotentiallysub-stratesforHR,butthemechanismsbywhichHRpromotesforkrestartandrecoveryremainunclear.Forkincisiontogenerateasingle-sidedDSBendorassDNAgapcouldinitiateHRFigure2).Therelativesignicanceofforkin-cisionversusgaprepairisuncertain,althoughFabreetal.(51)suggestedthatbreaksarerareinSphaseandthatssDNAgapsaretheprimarysubstratesforreplication-associatedHRinS.cerevisiae.Nevertheless,Hanadaetal.(63,64)andFrogetetal.(55)implicateMUS81-EME1inforkincisioninhumancellsandS.pomberespectively.DSBsareobservedafter18hofchronicHUchallenge,dependentonhumanMUS81-EME1(63).Interestingly,S.pombeMus81dissociatesfromchromatininresponsetoHUtreatment,althoughMus81isrequiredRegulationofHomologousRecombination129 GE44CH06-HeyerARI3October201011:50 forresistancetoHU(16,85).ItwasproposedthatforkincisionbyMus81-Mms4/EME1rep-resentsalastresortforforkrecovery,anditmaybenegativelyregulatedundersomecir-cumstancesofreplicationstress(85).dHJsareintermediatesduringmitoticDSBrepairbyHR(25).AlternativemechanismsforremovingdHJsdeterminewhetherthegeneticproductsresultinacrossoverornoncrossoveroutcome(Figure1).AnumberofconservedeukaryoticendonucleaseshavebeenproposedtocutHollidayjunctionsortheirprecursorsinvivo,includingS.cerevisiaeMus81-Mms4(hu-manMUS81-EME1),S.cerevisiaeYen1(hu-manGEN1),andSlx1-Slx4(Figure1)(104).Inadditiontoendonucleolyticresolution,dHJscanbedissolvedbytheconcertedactivitiesofahelicase-topoisomerasecomplex(Figure1(165).HowendonucleolyticresolutionofdHJsisregulatedrelativetodissolutionisunknown.Casparietal.(28)suggestedthatCDKphos-phorylatesTop3inS.pombe,dependentonin-teractionwiththeDDRmediatorCrb2.LossofTop3functionresultsinhyper-recombinationandcelldeathafterIR,perhapsassociatedwithaninabilitytooptimallyresolvedHJs.Insummary,nucleolyticprocessingofstalledreplicationforksanddHJsdetermineswhetherHRisinitiatedafterforkstallingandwhetherthegeneticoutcomeofHRispoten-tiallyacrossover.Theprocessesandproteinsinvolved,andtheirspecicfunctionandregu-lation,stillneedtobedetermined.MODEL:HOMOLOGOUSRECOMBINATION:APATHWAYWITHMETASTABLE,REVERSIBLEINTERMEDIATESTOACHIEVEFLEXIBILITYANDROBUSTNESSDNArepairisaformidabletaskthatrequiresqualitycontroltobalanceaccuracyoftherepaireventwiththepotentialforgenomerearrange-ments(87).Ithasbeenproposedthatreversibil-ityofHRintermediatesprovidesrobustnesstothepathway(87,148).Inbiology,theconceptofrobustnesshasbeenlargelydiscussedinthecontextofmutationalrobustness,keepinganorganismsphenotypeconstantinspiteofmu-tations(43).Inthepresentdiscussion,however,thetermrobustnessappliesmoreintheengi-neeringsense,whereasystemoralgorithmdoesnotbreakdowneasily,continuestooperatede-spitesingleapplicationfailures,andrecoversquicklyfrom,andholdsupunder,exceptionalcircumstances(4,131).WhatcanwelearnfromtheanalysisoftheregulationofHRaboutthemechanismofHRandhowitachievesrobustness?Oneas-pectisproteininteractions.Themyriadofdi-rectprotein-proteininteractionsbetweenHRproteinshavebeenpreviouslyprojectedintoasingletimepointandinterpretedasastablere-combinosome(66).Furtheranalysisnowsug-geststhattheseinteractionscanberegulatedbyreversibleposttranslationalmodications,aretransient,andoccursequentially(69,91,129,161),whichprovidessignicantlymoreplastic-ity.Asecondaspectispathwayexibility.WhiletheHRpathwayistypicallyportrayedasalinearFigure1revealsbifurcations,whereidenticalintermediates(D-loop,dHJ)canen-terdifferentsubpathwaysandfates.Finally,theabundanceofmotorproteinsthatdissociatere-combinationintermediatessuggeststhatappar-entantirecombinationmechanismsareintegralpartsoftheHRpathway.Fourkeyintermedi-atesinHRthatarereversiblebytheactionofmotorproteinsincludetheRad51-ssDNAla-ment,theinitialD-loop,theextendedD-loop,andthedHJ(Figure4).Theseintermediatesalsoappeartobemetastable,becausetheycanbevisualizedcytologically(Rad51foci)(97)oridentiedphysically(25,76,77).ThereissignicantevidencethatkeyHRin-termediatesarereversibleinvivoandthatthisfeatureisimportantforHR.Reversalofex-tendedD-loopsiscentraltotheSDSAmodelFigure1).Thereiscompellinggeneticevi-denceformultiple,sequentialDNA-strandin-vasioneventsduringHR,implyingdissocia-tionofD-loopsorextendedD-loops(3,139).Promiscuousjointformation,atleastinmei-oticHRinS.cerevisiae,isnotrareandneedsactivereversalbySgs1helicase(83,117)and130Heyer GE44CH06-HeyerARI3October201011:50 suppressionbyMMR(seeabove).Anotherindi-cationthatantirecombinationmechanismsareanintegralpartoftheHRpathwayispro-videdbythecomplexphenotypesofmutationsinHRmotorproteins.MutationsinS.cerevisiaeshowincreasedspontaneousrecombina-tionthatappearsunrelatedtocrossoversup-pression,whichisconsistentwiththeantire-combinationroleofSgs1,butreducedDNAdamageinducedrecombination,suggestingaprorecombinationrole(58).Likewise,yeastSrs2wasshowntohaveanti-andprorecombi-nationphenotypes,aswassuggestedforhumanFBH1(6,56,78,158).AdefectinC.eleganshumanRTEL1causeshyper-recombinationbutalsoaDNAdamagesensitivityprolethatsuggestsadefectinHR(11).TheFANCM-relatedproteins(humanFANCM,S.pombeS.cerevisiaeMph1)canreverseD-loopsinvitroand,dependingontheassay,mutantsdisplayanti-orprorecombinationphenotypes(10,60,102,121,125,133,162).Furthermore,thephenomenonofrecombination-dependentlethality,wherethesyntheticlethalityofcer-taindouble-mutantcombinations(e.g.,S.cere-visiaesrs2sgs1,mus81sgs1)canbesuppressedbyanHRdefect,demonstratestheoccurrenceofpotentiallytoxicHRintermediatesthatre-quireresolutionbynucleasesormotorproteins(51,58).InsummaryandasdepictedinFigure4,wesuggestthattheHRpathwayproceedsthroughaseriesofmetastable,reversibleintermediatesthatareunderactivepositiveandnegativereg-ulationtoallowexibilityfortherepairout-comes(crossoverversusnoncrossover),accom-modationoftheunforeseen(e.g.,absenceofasecondendandswitchtoBIR)(Figure1),andrecoveryfromunwantedintermediates(e.g.,in-dependentinvasionsofbothendsofaDSBintodifferenttargets),whichareallaspectsthatde-nerobustnessofawell-engineeredsystemthatisessentialformaintainingastablegenome.Reversibilityentailsthedestructionofpoten-tiallynormalintermediates(87),andtheMMRbarrier,forexample,affectsHRevenbetweenperfectlyhomologoussequences(112).Whilecounterintuitiveatrst,itappearsthatreac-tionsthatreverserecombinationintermediatesarerequiredfortheoptimalfunctioningofHR,asthestochasticnatureoftheprocesswillfavoraccuratepathwayprogression. SUMMARYPOINTS1.RecombinationalDNArepairisnotconstitutivebutishighlymodulatedbypositiveandapreponderanceofnegativeregulatorymechanisms.2.Twosignalingsystems,thecellcyclecontrolmachineryandtheDDR,intersectinthecontrolofHR.3.InDSBrepair,endresectionisamajorcommitmentpointtoHR,regulatedbyCDK-dependentphosphorylationofSae2/CtIP.4.TheRad51lamentisamajorregulatorycontrolpointofHRgovernedbymechanismsthatfavoritsassembly(mediatorsandtheirposttranslationalmodications)ordisassem-bly(antirecombinogenicmotorproteins).5.Severalmechanisms,includingMMR,extendedD-loopreversion,anddHJdissolution,enforceananticrossoverbiasduringDSBrepairinsomatic(mitotic)cells.6.AntirecombinationmechanismsmediatedbyDNAmotorproteinsappeartobeintegraltotheHRpathway,providingexibilityandrobustnessthroughreversible,metastableRegulationofHomologousRecombination131 GE44CH06-HeyerARI3October201011:50 DISCLOSURESTATEMENTTheauthorsarenotawareofanyafliations,memberships,funding,ornancialholdingsthatmightbeperceivedasaffectingtheobjectivityofthisreview.WethankSteveKowalczykowski,NeilHunter,andallmembersoftheHeyerlab(ShannonCeballos,ClareFasching,RyanJanke,DamonMeyer,ErinSchwartz,JessicaSneeden,WilliamWright,Xiao-PingZhang)forhelpfuldiscussionsandcriticalcomments.TheworkwassupportedbyNIH(GM58015,CA92776)andtheDoD(BC083684).J.L.issupportedbyaTRDRPpost-doctoralfellowship(17FT-0046).Weapologizethatnotalloftheoutstandingworkinthisareacouldbediscussedorcitedbecauseofspaceconstraints.LITERATURECITED1.AboussekhraA,ChanetR,AdjiriA,FabreF.1992.Semi-dominantsuppressorsofSrs2helicasemutationsSaccharomycescerevisiaemapinthegene,whosesequencepredictsaproteinwithsimilaritiestoprocaryoticRecAprotein.Mol.Cell.Biol.2.AboussekhraA,ChanetR,ZgagaZ,Cassier-ChauvatC,HeudeM,FabreF.1989.,ageneofSaccharomycescerevisiaeencodingaputativeDNAhelicaseinvolvedinDNArepair.Characteristicsofmutantsandsequenceofthegene.NucleicAcidsRes.3.AdamsMD,McVeyM,SekelskyJJ.2003.BLMindouble-strandbreakrepairbysynthesis-dependentstrandannealing.4.AlonU.2003.Biologicalnetworks:Thetinkererasanengineer.5.AstromSU,OkamuraSM,RineJ.1999.Yeastcell-typeregulationofDNArepair.6.AylonY,LiefshitzB,Bitan-BaninG,KupiecM.2003.MoleculardissectionofmitoticrecombinationintheyeastSaccharomycescerevisiaeMol.Biol.Cell 7,79.DemonstratetheimportanceofCDKactivityforregulatingDSBresectionandcommitmenttoHR. 7.AylonY,LiefshitzB,KupiecM.2004.TheCDKregulatesrepairofdouble-strandbreaksbyhomologousrecombinationduringthecellcycle.EMBOJ.8.BachratiCZ,BortsRH,HicksonID.2006.MobileD-loopsareapreferredsubstratefortheBloomssyndromehelicase.NucleicAcidsRes.9.BakkerST,vandeVrugtHJ,RooimansMA,OostraAB,SteltenpoolJ,etal.2009.Fancm-decientmicerevealuniquefeaturesofFanconianemiacomplementationgroupM.Hum.Mol.Genet.10.BanerjeeS,SmithS,OumJH,LiawHJ,HwangJY,etal.2008.Mph1ppromotesgrosschromosomalrearrangementthroughpartialinhibitionofhomologousrecombination.J.CellBiol.11.BarberLJ,YoudsJL,WardJD,McIlwraithMJ,ONeilNJ,etal.2008.RTEL1maintainsgenomicstabilitybysuppressinghomologousrecombination.12.BaroniE,ViscardiV,Cartagena-LirolaH,LucchiniG,LongheseMP.2004.ThefunctionsofbuddingyeastSae2intheDNAdamageresponserequireMec1-andTel1-dependentphosphorylation.Mol.Biol. 13,68.IdentifyRad55astargetofDDRsignalingandthatphosphorylationofRad55positivelyregulatesHR. 13.BashkirovVI,KingJS,BashkirovaEV,Schmuckli-MaurerJ,HeyerWD.2000.DNArepairproteinRad55isaterminalsubstrateoftheDNAdamagecheckpoints.Mol.Cell.Biol.14.BerginkS,JentschS.2009.PrinciplesofubiquitinandSUMOmodicationsinDNArepair.15.BernsteinK.GangloffS,RothsteinR.2010.TheRecQDNAhelicaseinDNArepair.Annu.Rev.Genet.16.BoddyMN,GaillardP-HL,McDonaldWH,ShanahanP,YatesJR3rd,RussellP.2001.Mus81-Eme1areessentialcomponentsofaHollidayjunctionresolvase.17.BranzeiD,FoianiM.2008.RegulationofDNArepairthroughoutthecellcycle.Nat.Rev.Mol.Cell.132Heyer GE44CH06-HeyerARI3October201011:50 18.BranzeiD,SollierJ,LiberiG,ZhaoXL,MaedaD,etal.2006.Ubc9-andmms21-mediatedsumoylationcounteractsrecombinogeniceventsatdamagedreplicationforks.19.BranzeiD,VanoliF,FoianiM.2008.SUMOylationregulatesRad18-mediatedtemplateswitch.20.BugreevDV,BroshRM,MazinAV.2008.RECQ1possessesDNAbranchmigrationactivity.J.Biol.21.BugreevDV,HanaokaF,MazinAV.2007.Rad54dissociateshomologousrecombinationintermediatesbybranchmigration.Nat.Struct.Mol.Biol.22.BugreevDV,MazinAV.2004.CaactivateshumanhomologousrecombinationproteinRad51bymodulatingitsATPaseactivity.Proc.Natl.Acad.Sci.USA23.BugreevDV,YuX,EgelmanEH,MazinAV.2007.Novelpro-andantirecombinationactivitiesoftheBloomssyndromehelicase.GenesDev.24.BusyginaV,SehornMG,ShiIY,TsubouchiH,RoederGS,SungP.2008.Hed1regulatesRad51-mediatedrecombinationviaanovelmechanism.GenesDev.25.BzymekM,ThayerNH,OhSD,KlecknerN,HunterN.2010.DoubleHollidayjunctionsareinterme-diatesofDNAbreakrepair.26.Cartagena-LirolaH,GueriniI,ViscardiV,LucchiniG,LongheseMP.2006.YeastSae2isaninvivotargetoftheMec1andTel1checkpointkinasesduringmeiosis.CellCycle27.CarterSD,VigasovaD,ChenJ,ChovanecM,AstromSU.2009.Nej1recruitstheSrs2helicasetoDNAdouble-strandbreaksandsupportsrepairbyasingle-strandannealing-likemechanism.Proc.Natl.Acad.Sci.USA28.CaspariT,MurrayJM,CarrAM.2002.Cdc2-cyclinBkinaseactivitylinksCrb2andRqh1-topoisomeraseGenesDev.29.ChanetR,HeudeM,AdjiriA,MaloiselL,FabreF.1996.SemidominantmutationsintheyeastRad51proteinandtheirrelationshipswiththeSrs2helicase.Mol.Cell.Biol.30.ChenFQ,NastasiA,ShenZY,BrennemanM,CrissmanH,ChenDJ.1997.Cellcycle-dependentproteinexpressionofmammalianhomologsofyeastDNAdouble-strandbreakrepairgenesRad51andMutat.Res.31.ChenW,Jinks-RobertsonS.1998.Mismatchrepairproteinsregulateheteroduplexformationduringmitoticrecombinationinyeast.Mol.Cell.Biol.32.ChioloI,SaponaroM,BaryshnikovaA,KimJH,SeoYS,LiberiG.2007.ThehumanF-BoxDNAhelicaseFBH1facesSaccharomycescerevisiaeSrs2andpostreplicationrepairpathwayroles.Mol.Cell.Biol.33.ColeGM,MortimerRK.1989.FailuretoinduceaDNArepairgene,,inSaccharomycescerevisiaedoesnotaffectDNArepairorrecombinationphenotypes.Mol.Cell.Biol.34.CooperJP,GreenwoodJ.2010.Telomericstrategies:meanstoanend.Annu.Rev.Genet.35.Cotta-RamusinoC,FachinettiD,LuccaC,DoksaniY,LopesM,etal.2005.Exo1processesstalledreplicationforksandcounteractsforkreversalincheckpoint-defectivecells.Mol.Cell36.CourcelleJ,KhodurskyA,PeterB,BrownPO,HanawaltPC.2001.ComparativegeneexpressionprolesfollowingUVexposureinwild-typeandSOS-decientEscherichiacoli37.DattaA,AdjiriA,NewL,CrouseGF,Jinks-RobertsonS.1996.MitoticcrossoversbetweendivergedsequencesareregulatedbymismatchrepairproteinsinSaccharomycescerevisiaeMol.Cell.Biol. 38.StudytheeffectsofmismatchesonHR,showingthatevenasinglemismtachhasan 38.DattaA,HendrixM,LipsitchM,Jinks-RobertsonS.1997.DualrolesforDNAsequenceidentityandthemismatchrepairsystemintheregulationofmitoticcrossing-overinyeast.Proc.Natl.Acad.Sci.USA39.DaviesAA,HuttnerD,DaigakuY,ChenS,UlrichHD.2008.Activationofubiquitin-dependentDNAdamagebypassismediatedbyreplicationproteinA.Mol.Cell40.DaviesAA,MassonJY,McIlwraithMJ,StasiakAZ,StasiakA,etal.2001.RoleofBRCA2incontroloftheRAD51recombinationandDNArepairprotein.Mol.Cell41.deJagerM,vanNoortJ,vanGentDC,DekkerC,KanaarR,WymanC.2001.HumanRad50/Mre11isaexiblecomplexthatcantetherDNAends.Mol.Cell42.deMayoloAA,LisbyM,ErdenizN,ThyboT,MortensenUH,RothsteinR.2006.MultiplestartcodonsandphosphorylationresultindiscreteRad52proteinspecies.NucleicAcidsRes.RegulationofHomologousRecombination133 GE44CH06-HeyerARI3October201011:50 43.DraghiJA,ParsonsTL,WagnerGP,PlotkinJB.2010.Mutationalrobustnesscanfacilitateadaptation.44.DrakeJW,CharlesworthB,CharlesworthD,CrowJF.1998.Ratesofspontaneousmutation.45.DupaigneP,LeBretonC,FabreF,GiangloffS,LeCamE,VeauteX.2008.TheSrs2helicaseac-tivityisstimulatedbyRad51lamentsondsDNA:ImplicationsforcrossoverincidenceduringmitoticMol.Cell46.EhmsenKT,HeyerWD.2008.Biochemistryofmeioticrecombination.InRecombinationandMeiosised.D-HLankenau,REgel,pp.91164.Berlin/Heidelberg:Springer-Verlag47.EladadS,YeTZ,HuP,LevershaM,BerestenS,etal.2005.Intra-nucleartrafckingoftheBLMhelicasetoDNAdamage-inducedfociisregulatedbySUMOmodication.Hum.Mol.Genet.48.El-ShemerlyM,HessD,PyakurelAK,MoselhyS,FerrariS.2008.ATR-dependentpathwayscontrolhEXO1stabilityinresponsetostalledforks.NucleicAcidsRes. 49.IdentiÞesthatphosphorylationofBRCA2inhibitsitsinteractionwithRAD51throughitsC-terminal 49.EsashiF,ChristN,GannonJ,LiuYL,HuntT,etal.2005.CDK-dependentphosphorylationofBRCA2asaregulatorymechanismforrecombinationalrepair.50.FabreF.1978.InducedintragenicrecombinationinyeastcanoccurduringtheG1mitoticphase.51.FabreF,ChanA,HeyerWD,GangloffS.2002.AlternatepathwaysinvolvingSgs1/Top3,Mus81/Mms4,andSrs2preventformationoftoxicrecombinationintermediatesfromsingle-strandedgapscreatedbyDNAreplication.Proc.Natl.Acad.Sci.USA52.FanningE,KlimovichV,NagerAR.2006.AdynamicmodelforreplicationproteinA(RPA)functioninDNAprocessingpathways.NucleicAcidsRes.53.Frank-VaillantM,MarcandS.2001.NHEJregulationbymatingtypeisexercisedthroughanovelprotein,Lif2p,essentialtotheligaseIVpathway.GenesDev.54.Frank-VaillantM,MarcandS.2002.TransientstabilityofDNAendsallowsnonhomologousendjoiningtoprecedehomologousrecombination.Mol.Cell55.FrogetB,BlaisonneauJ,LambertS,BaldacciG.2008.CleavageofstalledforksbyssionyeastMus81/Eme1inabsenceofDNAreplicationcheckpoint.Mol.Biol.Cell56.FuggerK,MistrikM,DanielsenJR,DinantC,FalckJ,etal.2009.HumanFbh1helicasecontributestogenomemaintenanceviapro-andantirecombinaseactivities.J.CellBiol.57.GalantyY,BelotserkovskayaR,CoatesJ,PoloS,MillerKM,JacksonSP.2009.MammalianSUMOE3-ligasesPIAS1andPIAS4promoteresponsestoDNAdouble-strandbreaks.58.GangloffS,SoustelleC,FabreF.2000.HomologousrecombinationisresponsibleforcelldeathintheabsenceoftheSgs1andSrs2helicases.Nat.Genet.59.GariK,DecailletC,DelannoyM,WuL,ConstantinouA.2008.RemodelingofDNAreplicationstructuresbythebranchpointtranslocaseFANCM.Proc.Natl.Acad.Sci.USA60.GariK,DecailletC,StasiakAZ,StasiakA,ConstantinouA.2008.TheFanconianemiaproteinFANCMcanpromotebranchmigrationofHollidayjunctionsandreplicationforks.Mol.Cell61.GildemeisterOS,SageJM,KnightKL.2009.CellularredistributionofRad51inresponsetoDNAdamage.NovelroleforRAD51C.J.Biol.Chem.62.GravelS,ChapmanJR,MagillC,JacksonSP.2008.DNAhelicasesSgs1andBLMpromoteDNAdouble-strandbreakresection.GenesDev.63.HanadaK,BudzowskaM,DaviesSL,vanDrunenE,OnizawaH,etal.2007.Thestructure-specicendonucleaseMus81contributestoreplicationrestartbygeneratingdouble-strandDNAbreaks.Struct.Mol.Biol.64.HanadaK,BudzowskaM,ModestiM,MaasA,WymanC,etal.2006.Thestructure-specicendonu-cleaseMus81-Eme1promotesconversionofinterstrandDNAcrosslinksintodouble-strandsbreaks.EMBOJ.65.HarfeBD,Jinks-RobertsonS.2000.DNAmismatchrepairandgeneticinstability.Annu.Rev.Genet.66.HaysSL,FirmenichAA,BergP.1995.Complexformationinyeastdouble-strandbreakrepair:Partic-ipationofRad51,Rad52,Rad55,andRad57proteins.Proc.Natl.Acad.Sci.USA134Heyer GE44CH06-HeyerARI3October201011:50 67.HellerRC,MariansKJ.2006.Replicationforkreactivationdownstreamofablockednascentleading68.HerzbergK,BashkirovVI,RolfsmeierM,HaghnazariE,McDonaldWH,etal.2006.Phospho-rylationofRad55onserines2,8,and14isrequiredforefÞcienthomologousrecombinationintherecoveryofstalledreplicationforks.Mol.Cell.Biol.69.HeyerWD.2007.Biochemistryofeukaryotichomologousrecombination.InMolecularGeneticsofRe-,ed.AAguilera,RRothstein,pp.95133.Berlin/Heidelberg:Springer-Verlag70.HeyerWD,LiX,RolfsmeierM,ZhangXP.2006.Rad54:theSwissArmyknifeofhomologousrecom-NucleicAcidsRes.71.HoeijmakersJHJ.2001.Genomemaintenancemechanismsforpreventingcancer.72.HolzenTM,ShahPP,OlivaresHA,BishopDK.2006.Tid1/Rdh54promotesdissociationofDmc1fromnonrecombinogenicsitesonmeioticchromatin.GenesDev.73.HuY,RaynardS,SehornMG,LuX,BussenW,etal.2007.RECQL5/Recql5helicaseregulatesho-mologousrecombinationandsuppressestumorformationviadisruptionofRad51presynapticlaments.GenesDev. 74,75.IdentifySae2/CtIPasthekeyCDKtargettocontrolDSBendresection. 74.HuertasP,Cortes-LedesmaF,SartoriAA,AguileraA,JacksonSP.2008.CDKtargetsSae2tocontrolDNA-endresectionandhomologousrecombination.75.HuertasP,JacksonSP.2009.HumanCtIPmediatescellcyclecontrolofDNAendresectionanddoublestrandbreakrepair.J.Biol.Chem.76.HunterN.2007.Meioticrecombination.InHomologousRecombination,ed.AAguilera,RRothstein,pp.381441.Berlin/Heidelberg:Springer-Verlag77.HunterN,KlecknerN.2001.Thesingle-endinvasion:anasymmetricintermediateatthedoublestrandbreaktodoubleHollidayjunctiontransitionofmeioticrecombination.78.IraG,MalkovaA,LiberiG,FoianiM,HaberJE.2003.Srs2andSgs1-Top3suppresscrossoversduringdouble-strandbreakrepairinyeast.79.IraG,PellicioliA,BalijjaA,WangX,FioraniS,etal.2004.DNAendresection,homologousrecombinationandDNAdamagecheckpointactivationrequireCDK1.80.IvanovEL,SugawaraN,FishmanlobellJ,HaberJE.1996.Geneticrequirementsforthesingle-strandannealingpathwayofdouble-strandbreakrepairinSaccharomycescerevisiae81.JainS,SugawaraN,LydeardJ,VazeM,TanguyLeGacN,HaberJE.2009.ArecombinationexecutioncheckpointregulatesthechoiceofhomologousrecombinationpathwayduringDNAdouble-strandbreakrepair.GenesDev.82.JankeR,HerzbergK,RolfsmeierM,MarJ,BashkirovVI,etal.2010.AtruncatedDNAdamagesignalingresponseisactivatedafterDSBformationintheG1phaseofSaccharomycescerevisiaeNucleicAcidsRes.83.JessopL,LichtenM.2008.Mus81/Mms4endonucleaseandSgs1helicasecollaboratetoensureproperrecombinationintermediatemetabolismduringmeiosis.Mol.Cell84.KadykLC,HartwellLH.1992.Sisterchromatidsarepreferredoverhomologsassubstratesforrecom-binationalrepairinSaccharomycescerevisiae85.KaiM,BoddyMN,RussellP,WangTSF.2005.ReplicationcheckpointkinaseCds1regulatesMus81toreservegenomeintegrityduringreplicationstress.GenesDev.86.KanaarR,TroelstraC,SwagemakersSMA,EssersJ,SmitB,etal.1996.HumanandmousehomologsoftheSaccharomycescerevisiaeRAD54DNArepairgene:Evidenceforfunctionalconservation.Curr.Biol.87.KanaarR,WymanC,RothsteinR.2008.QualitycontrolofDNAbreakmetabolism:intheend,itsagoodthing.EMBOJ.88.KeeY,KimJM,DAndreaA.2009.RegulateddegradationofFANCMintheFanconianemiapathwayduringmitosis.GenesDev.89.KolodnerRD,PutnamCD,MyungK.2002.MaintenanceofgenomestabilityinSaccharomycescerevisiae 90,158.DeterminethattheantirecombinaseSrs2dissociatesRad51fromssDNA. 90.KrejciL,VanKomenS,LiY,VillemainJ,ReddyMS,etal.2003.DNAhelicaseSrs2disruptstheRad51presynapticÞlament.RegulationofHomologousRecombination135 GE44CH06-HeyerARI3October201011:50 91.KroghBO,SymingtonLS.2004.Recombinationproteinsinyeast.Annu.Rev.Genet.92.LeeSE,MooreJK,HolmesA,UmezuK,KolodnerRD,HaberJE.1998.mre11/rad50andRPAproteinsregulateadaptationtoG2/MarrestafterDNAdamage.93.LeeSE,PaquesF,SylvanJ,HaberJE.1999.RoleofyeastSIRgenesandmatingtypeindirectingDNAdouble-strandbreakstohomologousandnonhomologousrepairpaths.Curr.Biol.94.LengsfeldBM,RattrayAJ,BhaskaraV,GhirlandoR,PaullTT.2007.Sae2isanendonucleasethatprocesseshairpinDNAcooperativelywiththeMre11/Rad50/Xrs2complex.Mol.Cell95.LiX,HeyerWD.2008.HomologousrecombinationinDNArepairandDNAdamagetolerance.96.Deletedinproof97.LisbyM,BarlowJH,BurgessRC,RothsteinR.2004.ChoreographyoftheDNAdamageresponse:Spatiotemporalrelationshipsamongcheckpointandrepairproteins.98.LopesM,FoianiM,SogoJM.2006.MultiplemechanismscontrolchromosomeintegrityafterreplicationforkuncouplingandrestartatirreparableUVlesions.Mol.Cell99.LuSP,LinSJ.2010.RegulationofyeastsirtuinsbyNAD()metabolismandcalorierestriction.Biophys.Acta100.MalkovaA,NaylorML,YamauchiM,IraG,HaberJE.2005.RAD51-dependentbreak-inducedrepli-cationdiffersinkineticsandcheckpointresponsesfromRAD51-mediatedgeneconversion.Mol.Biol.101.MalumbresM,BarbacidM.2005.Mammaliancyclin-dependentkinases.TrendsBiochem.Sci.102.MankouriHW,NgoHP,HicksonID.2009.Esc2andSgs1actinfunctionallydistinctbranchesofthehomologousrecombinationrepairpathwayinSaccharomycescerevisiaeMol.Biol.Cell103.MimitouEP,SymingtonLS.2008.Sae2,Exo1andSgs1collaborateinDNAdouble-strandbreakpro-104.MimitouEP,SymingtonLS.2009.Nucleasesandhelicasestakecenterstageinhomologousrecombi-TrendsBiochem.Sci.105.MoldovanG-L,DAndreaAD.2009.HowtheFanconianemiapathwayguardsthegenome.Annu.Rev.106.MorinI,NgoHP,GreenallA,ZubkoMK,MorriceN,LydallD.2008.Checkpoint-dependentphos-phorylationofExo1modulatestheDNAdamageresponse.EMBOJ.107.MorrisJR,BoutellC,KepplerM,DenshamR,WeekesD,etal.2009.TheSUMOmodicationpathwayisinvolvedintheBRCA1responsetogenotoxicstress.108.MorrisonC,SonodaE,TakaoN,ShinoharaA,YamamotoK,TakedaS.2000.ThecontrollingroleofATMinhomologousrecombinationalrepairofDNAdamage.EMBOJ.109.MortimerRK.1958.Radiobiologicalandgeneticstudiesonapolyploidseries(haploidtohexaploid)ofSaccharomycescerevisiaeRadiat.Res.110.MyungK,DattaA,ChenC,KolodnerRD.2001.,theSaccharomycescerevisiaehomologueof,suppressesgenomeinstabilityandhomeologousrecombination.Nat.Genet.111.NasmythK,HaeringCH.2009.Cohesin:itsrolesandmechanisms.Annu.Rev.Genet.112.NegrittoMT,WuXL,KuoT,ChuS,BailisAM.1997.InuenceofDNAsequenceidentityonefciencyoftargetedgenereplacement.Mol.Cell.Biol.113.NicholsonA,HendrixM,Jinks-RobertsonS,CrouseGF.2000.Regulationofmitotichomeologousrecombinationinyeast:Functionsofmismatchrepairandnucleotideexcisionrepairgenes.114.NimonkarAV,OzsoyAZ,GenschelJ,ModrichP,KowalczykowskiSC.2008.Humanexonuclease1andBLMhelicaseinteracttoresectDNAandinitiateDNArepair.Proc.Natl.Acad.Sci.USA115.NiuH,WanL,BusyginaV,KwonY,AllenJA,etal.2009.RegulationofmeioticrecombinationviaMek1-mediatedRad54phosphorylation.Mol.Cell116.NybergKA,MichelsonRJ,PutnamCW,WeinertTA.2002.Towardmaintainingthegenome:DNAdamageandreplicationcheckpoints.Annu.Rev.Genet.117.OhSD,LaoJP,HwangPYH,TaylorAF,SmithGR,HunterN.2007.BLMortholog,Sgs1,preventsaberrantcrossing-overbysuppressingformationofmultichromatidjointmolecules.136Heyer GE44CH06-HeyerARI3October201011:50 118.OsleyMA,TsukudaT,NickoloffJA.2007.ATP-dependentchromatinremodelingfactorsandDNAdamagerepair.Mutat.Res.119.OsmanF,DixonJ,BarrAR,WhitbyMC.2005.TheF-BoxDNAhelicaseFbh1preventsRhp51-dependentrecombinationwithoutmediatorproteins.Mol.Cell.Biol.120.OuyangKJ,WooLL,ZhuJM,HuoDZ,MatunisMJ,EllisNA.2009.SUMOmodicationregulatesBLMandRAD51interactionatdamagedreplicationforks.PLoSBiol.121.PanicoER,EdeC,SchildmannM,SchurerKA,KramerW.2010.GeneticevidenceforaroleofSaccharomycescerevisiaeMph1inrecombinationalDNArepairunderreplicativestress. 122,124.ShowthatsumoylatedPCNArecruitstheSrs2 122.PapouliE,ChenSH,DaviesAA,HuttnerD,KrejciL,etal.2005.CrosstalkbetweenSUMOandubiquitinonPCNAismediatedbyrecruitmentofthehelicaseSrs2p.Mol.Cell123.PaquesF,HaberJE.1999.Multiplepathwaysofrecombinationinducedbydouble-strandbreaksinSaccharomycescerevisiaeMicrobiol.Mol.Biol.Rev.124.PfanderB,MoldovanGL,SacherM,HoegeC,JentschS.2005.SUMO-modiÞedPCNArecruitsSrs2topreventrecombinationduringSphase.125.PrakashR,SatoryD,DrayE,PapushaA,SchellerJ,etal.2009.YeastMph1helicasedissociatesRad51-madeD-loops:implicationsforcrossovercontrolinmitoticrecombination.GenesDev.126.PrakashS,JohnsonRE,PrakashL.2005.EukaryotictranslesionsynthesisDNApolymerases:Specicityofstructureandfunction.Annu.Rev.Biochem.127.RosadoIV,NiedzwiedzW,AlpiAF,PatelKJ.2009.TheWalkerBmotifinavianFANCMisrequiredtolimitsisterchromatidexchangesbutisdispensableforDNAcrosslinkrepair.NucleicAcidsRes. 128,152.ShowthatRad52sumoylationcontrolsproteinstabilityand 128.SacherM,PfanderB,HoegeC,JentschS.2006.ControlofRad52recombinationactivitybydouble-strandbreak-inducedSUMOmodiÞcation.Nat.CellBiol.129.SanFilippoJ,SungP,KleinH.2008.Mechanismofeukaryotichomologousrecombination.Annu.Rev.130.SartoriAA,LukasC,CoatesJ,MistrikM,FuS,etal.2007.HumanCtIPpromotesDNAendresection.131.SavageauM.1971.Parametersensitivityasacriterionforevaluatingandcomparingtheperformanceofbiochemicalsystems.132.SchiestlRH,PrakashS,PrakashL.1990.ThesuppressorofmutationsofactsbychannelingDNAlesionsintotheDNArepairpathway.133.SchurerKA,RudolphC,UlrichHD,KramerW.2004.YeastMPH1genefunctionsinanerror-freeDNAdamagebypasspathwaythatrequiresgenesfromhomologousrecombination,butnotfrompostreplica-tiverepair.134.SeetBT,DikicI,ZhouMM,PawsonT.2006.Readingproteinmodicationswithinteractiondomains.Nat.Rev.Mol.Cell.Biol.135.SharanSK,MorimatsuM,AlbrechtU,LimDS,RegelE,etal.1997.EmbryoniclethalityandradiationhypersensitivitymediatedbyRad51inmicelackingBrca2.136.SharmaS,BroshRMJr.2007.HumanRECQ1isaDNAdamageresponsiveproteinrequiredforgenotoxicstressresistanceandsuppressionofsisterchromatidexchanges.PLoSOne137.SharmaS,StumpoDJ,BalajeeAS,BockCB,LansdorpPM,etal.2007.RECQL,amemberoftheRecQfamilyofDNAhelicases,suppresseschromosomalinstability.Mol.Cell.Biol.138.ShrivastavM,DeHaroLP,NickoloffJA.2008.RegulationofDNAdouble-strandbreakrepairpathwayCellRes.139.SmithCE,LlorenteB,SymingtonLS.2007.Templateswitchingduringbreak-inducedreplication.140.SommersJA,RawtaniN,GuptaR,BugreevDV,MazinAV,etal.2009.FANCJusesitsmotorATPasetodestabilizeprotein-DNAcomplexes,unwindtriplexes,andinhibitRAD51strandexchange.J.Biol.141.SørensenCS,HansenLT,DziegielewskiJ,SyljuasenRG,LundinC,etal.2005.Thecell-cyclecheck-pointkinaseChk1isrequiredformammalianhomologousrecombinationrepair.Nat.CellBiol.142.SpellRM,Jinks-RobertsonS.2004.ExaminationoftherolesofSgs1andSrs2helicasesintheenforce-mentofrecombinationdelityinSaccharomycescerevisiaeRegulationofHomologousRecombination137 GE44CH06-HeyerARI3October201011:50 143.StarkJM,PierceAJ,OhJ,PastinkA,JasinM.2004.Geneticstepsofmammalianhomologousrepairwithdistinctmutagenicconsequences.Mol.Cell.Biol.144.SugawaraN,GoldfarbT,StudamireB,AlaniE,HaberJE.2004.Heteroduplexrejectionduringsingle-strandannealingrequiresSgs1helicaseandmismatchrepairproteinsMsh2andMsh6butnotPms1.Proc.Natl.Acad.Sci.USA145.SugawaraN,WangX,HaberJE.2003.InvivorolesofRad52,Rad54,andRad55proteinsinRad51-mediatedrecombination.Mol.Cell146.SunW,NandiS,OsmanF,AhnJS,JakovleskaJ,etal.2008.TheFANCMorthologFml1promotesrecombinationatstalledreplicationforksandlimitscrossingoverduringDNAdouble-strandbreakMol.Cell147.SungP.1997.YeastRad55andRad57proteinsformaheterodimerthatfunctionswithreplicationproteinAtopromoteDNAstrandexchangebyRad51recombinase.GenesDev.148.SymingtonLS,HeyerWD.2006.Somedisassemblyrequired:roleofDNAtranslocasesinthedisruptionofrecombinationintermediatesanddead-endcomplexes.GenesDev.149.TayYD,SidebothamJM,WuL.2010.Mph1requiresmismatchrepair-independentand-dependentfunctionsofMutSalphatoregulatecrossoverformationduringhomologousrecombinationrepair.AcidsRes.150.TerasawaM,OgawaT,TsukamotoY,OgawaH.2008.Sae2pphosphorylationiscrucialforcooper-ationwithMre11pforresectionofDNAdouble-strandbreakendsduringmeioticrecombinationinSaccharomycescerevisiaeGenesGenet.Syst.151.TomitaK,MatsuuraA,CaspariT,CarrAM,AkamatsuY,etal.2003.CompetitionbetweentheRad50complexandtheKuheterodimerrevealsaroleforExo1inprocessingdouble-strandbreaksbutnotMol.Biol.Cell152.Torres-RosellJ,SunjevaricI,DePiccoliG,SacherM,Eckert-BouletN,etal.2007.TheSmc5-Smc6complexandSUMOmodiÞcationofRad52regulatesrecombinationalrepairattheribo-somalgenelocus.Nat.CellBiol.153.TrickeyM,GrimaldiM,YamanoH.2008.Theanaphase-promotingcomplex/cyclosomecontrolsrepairandrecombinationbyubiquitylatingRhp54inssionyeast.Mol.Cell.Biol.154.TrujilloKM,YuanSSF,LeeE,SungP.1998.NucleaseactivitiesinacomplexofhumanrecombinationandDNArepairfactorsRad50,Mre11,andp95.J.Biol.Chem.155.TsubouchiH,RoederGS.2006.BuddingyeastHed1down-regulatesthemitoticrecombinationma-chinerywhenmeioticrecombinationisimpaired.GenesDev.156.Valencia-BurtonM,OkiM,JohnsonJ,SeierTA,KamakakaR,HaberJE.2006.Differentmating-type-regulatedgenesaffecttheDNArepairdefectsofRAD51,RAD52andRAD55mutants.157.vanAttikumH,GasserSM.2009.CrosstalkbetweenhistonemodicationsduringtheDNAdamageTrendsCellBiol.158.VeauteX,JeussetJ,SoustelleC,KowalczykowskiSC,LeCamE,FabreF.2003.TheSrs2helicasepreventsrecombinationbydisruptingRad51nucleoproteinÞlaments.159.WardJD,MuzziniDM,PetalcorinMIR,Martinez-PerezE,MartinJS,etal.2010.Overlappingmech-naismspromotepostsynapticRAD-51lamentdisassemblyduringmeioticdouble-strandbreakrepair.Mol.Cell160.Welz-VoegeleC,Jinks-RobertsonS.2008.Sequencedivergenceimpedescrossovermorethannon-crossovereventsduringmitoticgaprepairinyeast.161.WestSC.2003.Molecularviewsofrecombinationproteinsandtheircontrol.Nat.Rev.Mol.Cell.Biol.162.WhitbyMC.2010.TheFANCMfamilyofDNAhelicases/translocases.DNARepair163.WohlboldL,FisherRP.2009.Behindthewheelandunderthehood:Functionsofcyclin-dependentkinasesinresponsetoDNAdamage.DNARepair164.WorthL,ClarkS,RadmanM,ModrichP.1994.MismatchrepairproteinsMutSandMutLinhibitRecA-catalyzedstrandtransferbetweendivergedDNAs.Proc.Natl.Acad.Sci.USA138Heyer GE44CH06-HeyerARI3October201011:50 165.WuLJ,HicksonID.2003.TheBloomssyndromehelicasesuppressescrossing-overduringhomologous166.WuLJ,DaviesSL,LevittNC,HicksonID.2001.PotentialrolefortheBLMhelicaseinrecombinationalrepairviaaconservedinteractionwithRAD51.J.Biol.Chem.167.WuY,KantakeN,SugiyamaT,KowalczykowskiSC.2008.Rad51proteincontrolsRad52-mediatedDNAannealing.J.Biol.Chem.168.YangHJ,LiQB,FanJ,HollomanWK,PavletichNP.2005.TheBRCA2homologueBrh2nucleatesRAD51lamentformationatadsDNA-ssDNAjunction.169.YoudsJL,BarberLJ,WardJD,CollisSJ,ONeilNJ,etal.2008.DOG-1istheCaenorhabditiselegansBRIP1/FANCJhomologueandfunctionsininterstrandcross-linkrepair.Mol.Cell.Biol.170.YoudsJL,MetsDG,McIlwraithMJ,MartinJS,WardJD,etal.2010.RTEL-1enforcesmeioticcrossoverinterferenceandhomeostasis.171.YuX,ChenJ.2004.DNAdamage-inducedcellcyclecheckpointcontrolrequiresCtIP,aphosphorylation-dependentbindingpartnerofBRCA1C-terminaldomains.Mol.Cell.Biol.172.YuX,FuS,LaiM,BaerR,ChenJ.2006.BRCA1ubiquitinatesitsphosphorylation-dependentbindingpartnerCtIP.GenesDev.173.YunMH,HiomK.2009.CtIP-BRCA1modulatesthechoiceofDNAdouble-strand-breakrepairpath-waythroughoutthecellcycle.174.ZhuZ,ChungWH,ShimEY,LeeSE,IraG.2008.Sgs1helicaseandtwonucleasesDna2andExo1resectDNAdouble-strandbreakends.RegulationofHomologousRecombination139 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