RNA-Chromatin Interactions: Methods and Protocols PDF
Preview RNA-Chromatin Interactions: Methods and Protocols
Methods in Molecular Biology 2161 Ulf Andersson Vang Ørom Editor RNA-Chromatin Interactions Methods and Protocols 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. RNA-Chromatin Interactions Methods and Protocols Edited by Ulf Andersson Vang Ørom Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark Editor UlfAnderssonVangØrom DepartmentforMolecularBiology andGenetics AarhusUniversity AarhusC,Denmark ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-0679-7 ISBN978-1-0716-0680-3 (eBook) https://doi.org/10.1007/978-1-0716-0680-3 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. 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Preface RNAisanessentialmoleculefornumerousbiologicalprocesses.Researchinrecentyearshas taughtusthatRNA–proteininteractionsplayanimportantroleforbothRNAandprotein function.WiththefocusonnoncodingRNAandtheirfunction,thenuclearandchromatin- associatedfunctionofRNAhasreceivedincreasingattention.Itismyhopethatresearchers interested in RNA-chromatin interactions and functionality can use this book as a starting pointtoexpandtheirexperimentalapproachestowardthenumerousoutstandingquestions inthisnewandexpandingfield. AarhusC,Denmark UlfAnderssonVangØrom v Contents Preface ..................................................................... v Contributors................................................................. ix 1 TuningtheExpressionofLongNoncodingRNALociwith CRISPRInterference.................................................... 1 LovorkaStojic 2 IdentificationofChromatinBindingSitesforLongNoncoding RNAsbyChromatinOligo-AffinityPrecipitation(ChOP) ................... 17 MariannaNicolettaRossiandRossellaMaione 3 KnockdownofNuclearlncRNAsbyLockedNucleicAcid(LNA) GapmersinNephronProgenitorCells..................................... 29 MasakiNishikawaandNorimotoYanagawa 4 DesignandApplicationofaShort(16-mer)LockedNucleicAcid Splice-SwitchingOligonucleotideforDystrophinProductionin DuchenneMuscularDystrophyMyotubes ................................. 37 Ce´liaCarvalhoandMariaCarmo-Fonseca 5 TargetingPolyadenylationforRetentionofRNAatChromatin............... 51 EvgeniaNtiniandUlfAnderssonVangØrom 6 SimultaneousDetectionofRNAsandProteinswith SubcellularResolution................................................... 59 SunjongKwon,KoeiChin,andMichelNederlof 7 InVivoCrosslinkingofHistoneandRNA-BindingProteins ................. 75 Yong-EunKim,KyoonEonKim,andKeeK.Kim 8 Proteomics-BasedSystematicIdentificationofNuclearProteins AnchoredtoChromatinviaRNA......................................... 89 KyokoHiragami-Hamada,NaokiTani,andJun-ichiNakayama 9 2DSaturationTransferDifferenceNMRforDeterminationof ProteinBindingSitesonRNAGuanineQuadruplexes....................... 101 EwanK.S.McRae,DavidE.Davidson,andSeanA.McKenna 10 MappingTranscriptome-Wide andGenome-WideRNA–DNA ContactswithChromatin-AssociatedRNASequencing(ChAR-seq) .......... 115 CharlesLimouse,DavidJukam,OwenK.Smith, KelseyA.Fryer,andAaronF.Straight 11 Identificationofcis-ElementsforRNASubcellularLocalization ThroughREL-seq ...................................................... 143 YafeiYinandXiaohuaShen 12 Transcriptome-Wide MappingofProtein–RNAInteractions ................. 161 XianjuBiandXiaohuaShen vii viii Contents 13 ProximityRNA-seq:ASequencingMethodtoIdentify Co-localization ofRNA................................................................ 175 J¨orgMorfandStevenW.Wingett 14 ImmunoprecipitationofDNA:RNAHybridsUsingthe S9.6Antibody.......................................................... 195 HunterR.GibbonsandThomasM.Aune 15 CharacterizationofR-LoopStructuresUsingSingle-Molecule R-LoopFootprintingandSequencing..................................... 209 MaikaMaligandFredericChedin 16 AnalysisofRNA–DNATriplexStructuresInVitroandInVivo............... 229 AnnaPostepska-Igielska,AlenaBlank-Giwojna andIngridGrummt 17 AnalyzingRNA–DNATriplexFormationinChromatin ..................... 247 RodrigoMaldonadoandGernotLa€ngst 18 MappingRNA–ChromatinInteractionsInVivowithRNA-DamID........... 255 SethW.CheethamandAndreaH.Brand Index ...................................................................... 265 Contributors THOMASM.AUNE • VanderbiltUniversityMedicalCenter,Nashville,TN,USA XIANJUBI • DepartmentofBasicMedicalSciences,SchoolofMedicine,TsinghuaUniversity, Beijing,China ALENABLANK-GIWOJNA • DivisionofMolecularBiologyoftheCellII,GermanCancer ResearchCenter,DKFZ-ZMBHAlliance,Heidelberg,Germany ANDREAH.BRAND • TheGurdonInstituteandDepartmentofPhysiology,Developmentand Neuroscience,UniversityofCambridge,Cambridge,UK MARIACARMO-FONSECA • InstitutodeMedicinaMolecular,FaculdadedeMedicina, UniversidadedeLisboa,Lisbon,Portugal CE´LIACARVALHO • InstitutodeMedicinaMolecular,FaculdadedeMedicina,Universidade deLisboa,Lisbon,Portugal FREDERIC CHEDIN • DepartmentofMolecularandCellularBiologyandGenomeCenter, UniversityofCaliforniaDavis,Davis,CA,USA SETHW.CHEETHAM • MaterResearchInstitute-UniversityofQueensland,Woolloongabba, QLD,Australia KOEICHIN • OHSUCenter forSpatialSystemsBiomedicine,OregonHealthandSciences University,Portland,OR,USA;DepartmentofBiomedicalEngineering,OregonHealth andSciencesUniversity,Portland,OR,USA DAVIDE.DAVIDSON • DepartmentofChemistry,UniversityofManitoba,Winnipeg,MB, Canada KELSEYA.FRYER • DepartmentofBiochemistry,StanfordUniversitySchoolofMedicine, Stanford,CA,USA;DepartmentofGenetics,StanfordUniversitySchoolofMedicine, Stanford,CA,USA HUNTERR.GIBBONS • VanderbiltUniversityMedicalCenter,Nashville,TN,USA INGRID GRUMMT • DivisionofMolecularBiologyoftheCellII,GermanCancerResearch Center,DKFZ-ZMBHAlliance,Heidelberg,Germany KYOKOHIRAGAMI-HAMADA • DivisionofChromatinRegulation,NationalInstitutefor BasicBiology,Okazaki,Aichi,Japan;DepartmentofBasicBiology,SchoolofLifeScience, TheGraduateUniversityforAdvancedStudies(SOKENDAI),Okazaki,Aichi,Japan DAVIDJUKAM • DepartmentofBiology,StanfordUniversity,Stanford,CA,USA KEEK.KIM • DepartmentofBiochemistry,ChungnamNationalUniversity,Daejeon, RepublicofKorea KYOON EONKIM • DepartmentofBiochemistry,ChungnamNationalUniversity,Daejeon, RepublicofKorea YONG-EUNKIM • DepartmentofBiochemistry,ChungnamNationalUniversity,Daejeon, RepublicofKorea SUNJONGKWON • OHSUCenter forSpatialSystemsBiomedicine,OregonHealthand SciencesUniversity,Portland,OR,USA;DepartmentofBiomedicalEngineering,Oregon HealthandSciencesUniversity,Portland,OR,USA € GERNOT LANGST • BiochemistryCenterRegensburg,UniversityofRegensburg,Regensburg, Germany CHARLESLIMOUSE • DepartmentofBiochemistry,StanfordUniversitySchoolofMedicine, Stanford,CA,USA ix x Contributors ROSSELLA MAIONE • DepartmentofMolecularMedicine,SapienzaUniversityofRome, Rome,Italy RODRIGO MALDONADO • LaboratoriodeBiologı´aCelular yMolecularAplicada, UniversidadMayor,Temuco,Chile MAIKAMALIG • DepartmentofMolecularandCellularBiologyandGenomeCenter, UniversityofCaliforniaDavis,Davis,CA,USA;IntegrativeGeneticsandGenomics GraduateGroup,UniversityofCaliforniaDavis,Davis,CA,USA SEANA.MCKENNA • DepartmentofChemistry,UniversityofManitoba,Winnipeg,MB, Canada;DepartmentofBiochemistryandMedicalGenetics,UniversityofManitoba, Winnipeg,MB,Canada;ManitobaInstituteforMaterials,UniversityofManitoba, Winnipeg,MB,Canada EWANK.S.MCRAE • DepartmentofChemistry,UniversityofManitoba,Winnipeg,MB, Canada JO¨RGMORF • Wellcome-MRCCambridgeStemCellInstitute,Cambridge,UK JUN-ICHINAKAYAMA • DivisionofChromatinRegulation,NationalInstituteforBasic Biology,Okazaki,Aichi,Japan;DepartmentofBasicBiology,SchoolofLifeScience,The GraduateUniversityforAdvancedStudies(SOKENDAI),Okazaki,Aichi,Japan MICHELNEDERLOF • QuantitativeImagingSystems,Inc.,Pittsburgh,PA,USA MASAKINISHIKAWA • SchoolofEngineering,ChemicalSystemEngineering,Universityof Tokyo,Tokyo,Japan EVGENIANTINI • MaxPlanckInstituteforMolecularGenetics,Berlin,Germany;Freie Universita€tBerlin,Berlin,Germany ULFANDERSSONVANGØROM • DepartmentforMolecularBiologyandGenetics,Aarhus University,AarhusC,Denmark ANNAPOSTEPSKA-IGIELSKA • DivisionofMolecularBiologyoftheCellII,GermanCancer ResearchCenter,DKFZ-ZMBHAlliance,Heidelberg,Germany MARIANNANICOLETTAROSSI • DivisionofRheumatology,IRCCSBambinoGesu` Children’s Hospital,Rome,Italy XIAOHUASHEN • DepartmentofBasicMedicalSciences,SchoolofMedicine,Tsinghua University,Beijing,China OWENK.SMITH • DepartmentofBiochemistry,StanfordUniversitySchoolofMedicine, Stanford,CA,USA;DepartmentofChemicalandSystemsBiology,StanfordUniversity SchoolofMedicine,Stanford,CA,USA LOVORKASTOJIC • CancerResearchUKCambridgeInstitute,UniversityofCambridge,Li KaShingCentre,RobinsonWay,Cambridge,London,UK;CentreforCancerCelland MolecularBiology,BartsCancerInstitute,QueenMaryUniversityofLondon,London,UK AARONF.STRAIGHT • DepartmentofBiochemistry,StanfordUniversitySchoolofMedicine, Stanford,CA,USA;DepartmentofChemicalandSystemsBiology,StanfordUniversity SchoolofMedicine,Stanford,CA,USA NAOKITANI • LiaisonLaboratoryResearchPromotionCenter,InstituteofMolecular EmbryologyandGenetics,KumamotoUniversity,Kumamoto,Japan STEVENW.WINGETT • Bioinformatics,BabrahamInstitute,Cambridge,UK NORIMOTOYANAGAWA • MedicalandResearchServices,GreaterLosAngelesVeteransAffairs HealthcareSystematSepulveda,NorthHills,CA,USA;DavidGeffenSchoolofMedicine, UniversityofCaliforniaatLosAngeles,LosAngeles,CA,USA YAFEIYIN • DepartmentofBasicMedicalSciences,SchoolofMedicine,TsinghuaUniversity, Beijing,China
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