Yeast functional genomics : methods and protocols PDF
Preview Yeast functional genomics : methods and protocols
Methods in Molecular Biology 2477 Frédéric Devaux Editor Yeast Functional Genomics Methods and Protocols Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Yeast Functional Genomics Methods and Protocols Second Edition Edited by Frédéric Devaux Institut de Biologie Paris Seine, Sorbonne Université, Paris, France Editor Fre´de´ricDevaux InstitutdeBiologieParisSeine SorbonneUniversite´ Paris,France ISSN1064-3745 ISSN1940-6029 (electronic) ISBN978-1-0716-2256-8 ISBN978-1-0716-2257-5 (eBook) https://doi.org/10.1007/978-1-0716-2257-5 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2016,2022 Chapters 1, 9, 16, 20, 22, 24, and 25 are licensed under the terms of the Creative Commons Attribution 4.0 InternationalLicense(http://creativecommons.org/licenses/by/4.0/).For furtherdetailsseelicenseinformationin thechapter. Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductionon microfilmsorinanyotherphysicalway,andtransmissionorinformation storageand retrieval,electronicadaptation, computersoftware,orbysimilar ordissimilar methodologynow knownorhereafter developed. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLCpartofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface FiveyearsafterthefirsteditionoftheYeastFunctionalGenomics:MethodsandProtocolsissue of the Methods in Molecular Biology book series came out, it seems that the topic is more relevant and livelier than ever. Not only are the basics of yeast functional genomics still extensivelyusedbyhundredsoflaboratories,butnewtechniquesappearedthatscaledupthe powerofgenome-wideapproachesofyeastfunctioning. Third-generationsequencingdevicesgaveanewstarttoyeasttranscriptomicsbygiving accesstofull-lengthcDNAs,andevenallowdirectsequencingofRNAsandtheirchemical modifications,pavingthewaytoyeastepitranscriptomics. Transposon saturation, RNAi and CRISPR/cas assays empowered the already high potential for global genetic screens in yeast, looking for protein-protein interactions, and essential genes or gene-drug interactions. At the same time, yeast phenomics, i.e., high- throughputyeastphenotypicprofiling,whichappearedattheendofthefirstdecadeofthe century, has been automatized and now takes advantage of bar-coded strain collections allowingforaccuratelineagetracing. Alternatives to the classic chromatin immunoprecipitation-sequencing (ChIP-seq) approach, together with single cell transcriptomics and with the development of various techniquestodetectRNApolymeraseIIactivityallalongthegenome,havebeenchanging thewayweenvisionyeasttranscriptionalnetworks. Specificribosomeprofiling,tailoredandmorequantitativeproteomicswithsmarterway ofanalyzingnativeproteincomplexesarepushingourknowledgeoftranslationalregulatory networkstothesamelevelasthatoftheir transcriptionalcounterparts. The number of genomes available for yeast species jumped from 40 to more than 300,givingaccesstocomprehensivecomparativetranscriptomicsstudies. Finally, the time dedicated to in silico analyses in the daily practice of yeast functional “genomicists” has increased again, and the exponential increase in the amount of available data of various types (transcriptomics, proteomics, interactomics, ...) raises the crucial question of their integration into comprehensive and analytical databases, to prepare for their futureexplorationusingmachinelearningapproaches. The rationale guiding the elaboration of this second edition was to reflect all these recentevolutionsofthefieldandtomakeitascomplementarytothefirsteditionaspossible. Therefore,mostofthechaptersinthepresentvolumepresentnewtechniquesandprotocols that were not included in the first edition. Compared with the previous version, the part dedicated to in silico analyses increased and most protocols in this volume include a significant bioinformatics part. Some authors even provided their informatics scripts as supplementarymaterialavailablethroughtheonlineversionofthebook. Aswiththefirstedition,themaingoalofthesecondeditionwastomakeitinteresting and useful to the community of yeast researchers. I do hope that we reached this goal (again). Paris,France Fre´de´ricDevaux v Contents Preface ..................................................................... v Contributors................................................................. xi PART I TRANSCRIPTOMIC ANALYSES 1 Single-CellRNASequencinginYeastUsingthe10(cid:1)Genomics ChromiumDevice ...................................................... 3 LieselotteVermeersch,AbbasJariani,JanaHelsen, BenjaminM.Heineike,andKevinJ.Verstrepen 2 Genome-WideProfilingofTranscriptionInitiationwithSTRIPE-seq ......... 21 RobertA.Policastro andGabrielE.Zentner 3 AModifiedCross-LinkingAnalysisofcDNAs(CRAC)Protocol forDetectingRNA–ProteinInteractionsandTranscription atSingle-NucleotideResolution .......................................... 35 DriceChallal,JessieColin,TommasoVilla,andDomenicoLibri 4 High-ResolutionDeepSequencingofNascentTranscriptioninYeast withBioGRO-seq....................................................... 57 AntonioJorda´n-PlaandJose´E.Pe´rez-Ortı´n 5 DirectSequencingofRNAandRNAModificationIdentification UsingNanopore........................................................ 71 ThidathipWongsurawat,PiroonJenjaroenpun, andIntawatNookaew 6 UNAGI:YeastTranscriptomeReconstructionandGeneDiscovery UsingNanoporeSequencing............................................. 79 MohamadAlkadi,NicolasJung,andDaisukeOkuzaki 7 IdentificationofTaxonomicallyRestrictedTranscriptsfromIllumina RNASequencingData................................................... 91 WilliamR.Blevins PART II DNA REPLICATION AND PROTEIN/DNA INTERACTIONS 8 FORK-seq:Single-MoleculeProfilingofDNAReplication................... 107 MagaliHennion,BertrandTheulot,Jean-MichelArbona, BenjaminAudit,andOlivierHyrien 9 CUT&RUNProfilingoftheBuddingYeastEpigenome..................... 129 SandipanBrahmaandStevenHenikoff 10 ChIP-SICAP:ANewTooltoExploreGene-RegulatoryNetworks inCandidaalbicansandOtherYeasts..................................... 149 LassevanWijlick,AnshGoyal,SophieBachellier-Bassi, andChristophed’Enfert vii viii Contents PART III TRANSLATION DYNAMICS, PROTEIN COMPLEXES, AND PROTEOMICS 11 PurificationofRibosome-Nascent-ChainComplexforRibosomeProfiling andSelectiveRibosomeProfiling ......................................... 179 HagitBar-Yosef,JohannesVenezian,KevinKlann, andAyalaShiber 12 Single-StepAffinityPurification(ssAP)andMassSpectrometry ofMacromolecularComplexesintheYeastS.cerevisiae...................... 195 ChristianTrahanandMarleneOeffinger 13 CompositionandDynamicsofProteinComplexesMeasured byQuantitativeMassSpectrometryofAffinity-PurifiedSamples.............. 225 AbdelkaderNamaneandCosminSaveanu 14 DeepMutationalScanningofProtein–ProteinInteractions BetweenPartnersExpressedfromTheirEndogenousLociInVivo ........... 237 Alexandre K.Dube´,RohanDandage,SohamDibyachintan, UgoDionne,PhilippeC.Despre´s,andChristianR.Landry 15 ProteomicMappingbyAPEX2-CatalyzedProximityLabeling inSaccharomycescerevisiaeSemipermeabilizedCells ......................... 261 BirgitSinger-Kru¨gerandRalf-PeterJansen 16 QuantitativeProteomicsinYeast:FrombSLIMandProteomeDiscoverer OutputstoGraphicalAssessmentoftheSignificanceofProtein QuantificationScores.................................................... 275 NicolasSe´ne´caut,PierrePoulain,LaurentLignie`res, SamuelTerrier,Ve´roniqueLegros,GuillaumeChevreux, Ga¨elleLelandais,andJean-MichelCamadro 17 AStrongCationExchangeChromatographyProtocolforExamining N-TerminalProteoforms ................................................ 293 EsperanzaFerna´ndez,AnneliesBogaert,EvyTimmerman, AnStaes,FrancisImpens,andKrisGevaert PART IV GENOTYPIC SCREENS AND PHENOTYPIC PROFILING 18 RNAInterference(RNAi)asaToolforHigh-ResolutionPhenotypic ScreeningofthePathogenicYeastCandidaglabrata........................ 313 AndreasTsouris,JosephSchacherer,andOlenaP.Ishchuk 19 High-ThroughputGeneMutagenesisScreeningUsingBaseEditing.......... 331 PhilippeC.Despre´s,Alexandre K.Dube´,NozomuYachie, andChristianR.Landry 20 SAturatedTransposonAnalysisinYeast(SATAY)forDeepFunctional MappingofYeastGenomes .............................................. 349 Agne`sH.MichelandBenoıˆtKornmann 21 High-Throughput,High-PrecisionColonyPhenotypingwithPyphe .......... 381 StephanKamrad,Ju¨rgBa€hler,andMarkusRalser 22 Bulk-FitnessMeasurementsUsingBarcodeSequencingAnalysisinYeast ...... 399 ClaireA.ChochinovandAlexN.NguyenBa Contents ix PART V IN SILICO INTEGRATION OF FUNCTIONAL GENOMICS DATA 23 PredictionofGeneandGenomicRegulationinCandidaSpecies, UsingthePathoYeastractDatabase:AComparativeGenomicsApproach ...... 419 PedroPais,JorgeOliveira,RomeuViana,IneˆsV.Costa, IsabelSa´-Correia,PedroT.Monteiro, andMiguelC.Teixeira 24 EnablingStudiesofGenome-ScaleRegulatoryNetworkEvolution inLargePhylogenieswithMRTLE ....................................... 439 ShiluZhang,SaraKnaack,andSushmitaRoy 25 OmicsAnalyses:HowtoNavigateThroughaConstantDataDeluge ......... 457 ThomasDeneckerandGa¨elleLelandais Index ...................................................................... 473 Contributors MOHAMADALKADI • DepartmentofBacterialInfections,ResearchInstituteforMicrobial Diseases,OsakaUniversity,Osaka,Japan JEAN-MICHELARBONA • Universite´deLyon,CNRS,INSERM,LaboratoryofBiologyand ModellingoftheCell,Lyon,France BENJAMINAUDIT • UnivLyon,ENSdeLyon,CNRS,LaboratoiredePhysique,Lyon,France SOPHIE BACHELLIER-BASSI • Unite´BiologieetPathoge´nicite´Fongiques,De´partementde Mycologie,InstitutPasteur,USC2019INRAE,Paris,France JU¨RGBA€HLER • DepartmentofGenetics,EvolutionandEnvironment,InstituteofHealthy Ageing,UniversityCollegeLondon,London,UK HAGIT BAR-YOSEF • FacultyofBiology,Technion—IsraelInstituteofTechnology,Haifa, Israel WILLIAMR.BLEVINS • SingleCellGenomicsGroup,CentroNacionaldeAna´lisisGen(cid:2)omico (CNAG),Barcelona,Spain ANNELIESBOGAERT • VIBCenterforMedicalBiotechnology,Ghent,Belgium;Departmentof BiomolecularMedicine,GhentUniversity,Ghent,Belgium SANDIPANBRAHMA • BasicSciencesDivision,FredHutchinsonCancerResearchCenter, Seattle,WA,USA;HowardHughesMedicalInstitute,Seattle,WA,USA JEAN-MICHELCAMADRO • Mitochondria,Metals,andOxidativeStressGroup,Institut JacquesMonod,Universite´deParis—CNRS,Paris,France;ProteoSeine@IJM,Institut JacquesMonod,Universite´deParis—CNRS,Paris,France DRICECHALLAL • Universite´deParis,CNRS,InstitutJacquesMonod,Paris,France; InstitutCurie,PSLResearchUniversity,CNRSUMR3348,Orsay,France GUILLAUMECHEVREUX • ProteoSeine@IJM,InstitutJacquesMonod,Universite´deParis— CNRS,Paris,France CLAIREA.CHOCHINOV • DepartmentofCellandSystemsBiology,UniversityofToronto, Toronto,ON,Canada;DepartmentofBiology,UniversityofTorontoatMississauga, Mississauga,ON,Canada JESSIE COLIN • Universite´deParis,CNRS,InstitutJacquesMonod,Paris,France;Ecole PratiquedesHautesEtudes–PSLResearchUniversity,Paris,France;Unite´Biologiedes ARNdesPathoge`nesFongiques,InstitutPasteur,Paris,France INEˆSV.COSTA • iBB—InstituteforBioengineeringandBiosciences,BiologicalSciences ResearchGroup,InstitutoSuperiorTe´cnico,UniversidadedeLisboa,Lisbon,Portugal; DepartmentofBioengineering,InstitutoSuperiorTe´cnico,UniversidadedeLisboa,Lisbon, Portugal CHRISTOPHE D’ENFERT • Unite´BiologieetPathoge´nicite´Fongiques,De´partementde Mycologie,InstitutPasteur,USC2019INRAE,Paris,France ROHANDANDAGE • De´partementdeBiochimie,MicrobiologieetBio-informatique,Faculte´de SciencesetGe´nie,Universite´Laval,Que´bec,QC,Canada;PROTEO,leregroupementque´be´ coisderecherchesurlafonction,l’inge´nierieetlesapplicationsdesprote´ines,Universite´ Laval,Que´bec,QC,Canada;CentredeRechercheenDonne´esMassives(CRDM), Universite´Laval,Que´bec,QC,Canada;InstitutdeBiologieInte´grativeetdesSyste`mes, Universite´Laval,Que´bec,QC,Canada;De´partementdeBiologie,Faculte´deSciencesetGe´ nie,Universite´Laval,Que´bec,QC,Canada xi
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