RNA-Chromatin Interactions: Methods and Protocols

271 Pages·2020·7.175 MB·English

by  Ulf Andersson Vang Ørom

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
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School of Lifeand MedicalSciences
University ofHertfordshire
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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
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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