The Use of CRISPR/cas9, ZFNs, TALENs in Generating Site Specific Genome Alterations PDF
Preview The Use of CRISPR/cas9, ZFNs, TALENs in Generating Site Specific Genome Alterations
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON and MELVIN I. SIMON Division of Biology California Institute of Technology Pasadena, California ANNA MARIE PYLE Departments of Molecular, Cellular and Developmental Biology and Department of Chemistry Investigator Howard Hughes Medical Institute Yale University Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 225WymanStreet,Waltham,MA02451,USA 32JamestownRoad,LondonNW17BY,UK TheBoulevard,LangfordLane,Kidlington,Oxford,OX51GB,UK Firstedition2014 Copyright©2014ElsevierInc.Allrightsreserved. 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ISBN:978-0-12-801185-0 ISSN:0076-6879 ForinformationonallAcademicPresspublications visitourwebsiteatstore.elsevier.com CONTRIBUTORS CarolinAnders DepartmentofBiochemistry,UniversityofZurich,Zurich,Switzerland CarlosF.BarbasIII DepartmentofChemistry,andDepartmentofCellandMolecularBiology,TheSkaggs InstituteforChemicalBiology,TheScrippsResearchInstitute,LaJolla,California,USA IraL.Blitz DepartmentofDevelopmentalandCellBiology,UniversityofCalifornia,Irvine,California, USA ErikaBrunet MuseumNationald’HistoireNaturelle,INSERMU1154,CNRS7196,Paris,France SusanM.Byrne DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,USA JamieH.D.Cate EnergyBiosciencesInstitute;DepartmentofMolecularandCellBiology;Departmentof Chemistry,UniversityofCalifornia,andPhysicalBiosciencesDivision,LawrenceBerkeley NationalLaboratory,Berkeley,California,USA ReginaCencic DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada BaohuiChen DepartmentofPharmaceuticalChemistry,UniversityofCalifornia,SanFrancisco, California,USA KenW.Y.Cho DepartmentofDevelopmentalandCellBiology,UniversityofCalifornia,Irvine,California, USA GeorgeM.Church DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,USA ChadA.Cowan DepartmentofStemCellandRegenerativeBiology,HarvardUniversity;HarvardStemCell Institute,ShermanFairchildBiochemistry,Cambridge,andCenterforRegenerative Medicine,MassachusettsGeneralHospital,Boston,Massachusetts,USA D.Dambournet DepartmentofMolecularandCellBiology,UniversityofCalifornia,Berkeley,California, USA D.G.Drubin DepartmentofMolecularandCellBiology,UniversityofCalifornia,Berkeley,California, USA xiii xiv Contributors LeonardoM.R.Ferreira DepartmentofStemCellandRegenerativeBiology,HarvardUniversity,Cambridge, Massachusetts,USA MargaretB.Fish DepartmentofDevelopmentalandCellBiology,UniversityofCalifornia,Irvine,California, USA YanfangFu MolecularPathologyUnit,CenterforComputationalandIntegrativeBiology,andCenter forCancerResearch,MassachusettsGeneralHospital,Charlestown,andDepartmentof Pathology,HarvardMedicalSchool,Boston,Massachusetts,USA YoshitakaFujihara ResearchInstituteforMicrobialDiseases,OsakaUniversity,Suita,Japan ThomasGaj DepartmentofChemistry,andDepartmentofCellandMolecularBiology,TheSkaggs InstituteforChemicalBiology,TheScrippsResearchInstitute,LaJolla,California,USA HindGhezraoui MuseumNationald’HistoireNaturelle,INSERMU1154,CNRS7196,Paris,France AndrewP.W.Gonzales CardiovascularResearchCenter,MassachusettsGeneralHospital,Charlestown,and DepartmentofMedicine,HarvardMedicalSchool,Boston,Massachusetts,USA FedericoGonza´lez DevelopmentalBiologyProgram,Sloan-KetteringInstitute,NewYork,USA RobertM.Grainger DepartmentofBiology,UniversityofVirginia,Charlottesville,Virginia,USA A.Grassart DepartmentofMolecularandCellBiology,UniversityofCalifornia,Berkeley,California, USA YutingGuan ShanghaiKeyLaboratoryofRegulatoryBiology,InstituteofBiomedicalSciencesand SchoolofLifeSciences,EastChinaNormalUniversity,Shanghai,China JohnP.Guilinger DepartmentofChemistry&ChemicalBiology,andHowardHughesMedicalInstitute, HarvardUniversity,Cambridge,Massachusetts,USA S.H.Hong DepartmentofMolecularandCellBiology,UniversityofCalifornia,Berkeley,California, USA BenjaminE.Housden DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,USA BoHuang DepartmentofPharmaceuticalChemistry,andDepartmentofBiochemistryandBiophysics, UniversityofCalifornia,SanFrancisco,California,USA Contributors xv DanweiHuangfu DevelopmentalBiologyProgram,Sloan-KetteringInstitute,NewYork,USA MasahitoIkawa ResearchInstituteforMicrobialDiseases,OsakaUniversity,Suita,Japan RayelleItouaMa¨ıga DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada MariaJasin DevelopmentalBiologyProgram,MemorialSloan-KetteringCancerCenter,NewYork, USA MartinJinek DepartmentofBiochemistry,UniversityofZurich,Zurich,Switzerland J.KeithJoung MolecularPathologyUnit,CenterforComputationalandIntegrativeBiology,andCenter forCancerResearch,MassachusettsGeneralHospital,Charlestown,andDepartmentof Pathology,HarvardMedicalSchool,Boston,Massachusetts,USA AlexandraKatigbak DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada HyongbumKim GraduateSchoolofBiomedicalScienceandEngineering,CollegeofMedicine,Hanyang University,Seoul,SouthKorea Jin-SooKim CenterforGenomeEngineering,InstituteforBasicScience,andDepartmentofChemistry, SeoulNationalUniversity,Seoul,SouthKorea Young-HoonKim GraduateSchoolofBiomedicalScienceandEngineering,CollegeofMedicine,Hanyang University,Seoul,SouthKorea PrzemekM.Krawczyk DevelopmentalBiologyProgram,MemorialSloan-KetteringCancerCenter,NewYork, USA,andDepartmentofCellBiologyandHistology,AcademicMedicalCenter,University ofAmsterdam,Amsterdam,TheNetherlands DaliLi ShanghaiKeyLaboratoryofRegulatoryBiology,InstituteofBiomedicalSciencesand SchoolofLifeSciences,EastChinaNormalUniversity,Shanghai,China Jian-FengLi DepartmentofMolecularBiology,CentreforComputationalandIntegrativeBiology, MassachusettsGeneralHospital,andDepartmentofGenetics,HarvardMedicalSchool, Boston,Massachusetts,USA ShuailiangLin DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,USA xvi Contributors DavidR.Liu DepartmentofChemistry&ChemicalBiology,andHowardHughesMedicalInstitute, HarvardUniversity,Cambridge,Massachusetts,USA MingyaoLiu ShanghaiKeyLaboratoryofRegulatoryBiology,InstituteofBiomedicalSciencesand SchoolofLifeSciences,EastChinaNormalUniversity,Shanghai,China PrashantMali DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,USA AbbaMalina DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada PankajK.Mandal DepartmentofStemCellandRegenerativeBiology,HarvardUniversity,Cambridge,and PrograminCellularandMolecularMedicine,DivisionofHematology/Oncology,Boston Children’sHospital,Boston,Massachusetts,USA SumanthManohar DepartmentofBiology,UniversityofVirginia,Charlottesville,Virginia,USA TorstenB.Meissner DepartmentofStemCellandRegenerativeBiology,HarvardUniversity,Cambridge, Massachusetts,USA HisashiMiura DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada DanaC.Nadler DepartmentofChemicalandBiomolecularEngineering,UniversityofCalifornia,Berkeley, California,USA TakuyaNakayama DepartmentofBiology,UniversityofVirginia,Charlottesville,Virginia,USA BenjaminL.Oakes DepartmentofMolecular&CellBiology,UniversityofCalifornia,Berkeley,California, USA AkinleyeO.Odeleye DepartmentofBiology,UniversityofVirginia,Charlottesville,Virginia,USA VikramPattanayak DepartmentofPathology,MassachusettsGeneralHospital,Boston,Massachusetts,USA JerryPelletier DepartmentofBiochemistry;DepartmentofOncology,andTheRosalindandMorris GoodmanCancerResearchCenter,McGillUniversity,Montreal,Quebec,Canada NorbertPerrimon DepartmentofGenetics,andHowardHughesMedicalInstitute,HarvardMedicalSchool, Boston,Massachusetts,USA Contributors xvii MarionPiganeau MuseumNationald’HistoireNaturelle,INSERMU1154,CNRS7196,Paris,France BenjaminRenouf MuseumNationald’HistoireNaturelle,INSERMU1154,CNRS7196,Paris,France DeepakReyon MolecularPathologyUnit,CenterforComputationalandIntegrativeBiology,andCenter forCancerResearch,MassachusettsGeneralHospital,Charlestown,andDepartmentof Pathology,HarvardMedicalSchool,Boston,Massachusetts,USA FrancisRobert DepartmentofBiochemistry,McGillUniversity,Montreal,Quebec,Canada DerrickJ.Rossi DepartmentofStemCellandRegenerativeBiology,HarvardUniversity,Cambridge; PrograminCellularandMolecularMedicine,DivisionofHematology/Oncology,Boston Children’sHospital;DepartmentofPediatrics,HarvardMedicalSchool,Boston,and HarvardStemCellInstitute,ShermanFairchildBiochemistry,Cambridge,Massachusetts, USA OwenW.Ryan EnergyBiosciencesInstitute,UniversityofCalifornia,Berkeley,California,USA DavidF.Savage DepartmentofMolecular&CellBiology;DepartmentofChemistry,andEnergy BiosciencesInstitute,UniversityofCalifornia,Berkeley,California,USA HillelT.Schwartz DivisionofBiologyandBiologicalEngineering,CaliforniaInstituteofTechnology,and HowardHughesMedicalInstitute,Pasadena,California,USA YanjiaoShao ShanghaiKeyLaboratoryofRegulatoryBiology,InstituteofBiomedicalSciencesand SchoolofLifeSciences,EastChinaNormalUniversity,Shanghai,China JenSheen DepartmentofMolecularBiology,CentreforComputationalandIntegrativeBiology, MassachusettsGeneralHospital,andDepartmentofGenetics,HarvardMedicalSchool, Boston,Massachusetts,USA MinjungSong GraduateSchoolofBiomedicalScienceandEngineering,CollegeofMedicine,Hanyang University,Seoul,SouthKorea PaulW.Sternberg DivisionofBiologyandBiologicalEngineering,CaliforniaInstituteofTechnology,and HowardHughesMedicalInstitute,Pasadena,California,USA AlexandroE.Trevino BroadInstituteofMITandHarvard,7CambridgeCenter;McGovernInstituteforBrain Research;DepartmentofBrainandCognitiveSciences,andDepartmentofBiological Engineering,MassachusettsInstituteofTechnology,Cambridge,Massachusetts,USA xviii Contributors LianneE.M.Vriend DevelopmentalBiologyProgram,MemorialSloan-KetteringCancerCenter,NewYork, USA,andDepartmentofCellBiologyandHistology,AcademicMedicalCenter,University ofAmsterdam,Amsterdam,TheNetherlands Jing-RueyJoannaYeh CardiovascularResearchCenter,MassachusettsGeneralHospital,Charlestown,and DepartmentofMedicine,HarvardMedicalSchool,Boston,Massachusetts,USA DandanZhang DepartmentofMolecularBiology,CentreforComputationalandIntegrativeBiology, MassachusettsGeneralHospital,andDepartmentofGenetics,HarvardMedicalSchool, Boston,Massachusetts,USA FengZhang BroadInstituteofMITandHarvard,7CambridgeCenter;McGovernInstituteforBrain Research;DepartmentofBrainandCognitiveSciences,andDepartmentofBiological Engineering,MassachusettsInstituteofTechnology,Cambridge,Massachusetts,USA ZengrongZhu DevelopmentalBiologyProgram,Sloan-KetteringInstitute,NewYork,USA PREFACE The availability of whole-genome sequencing data for large numbers and types of organisms including humans holds exciting promise for advancing bothresearchandhealthcare.Amajorchallengehasbeenunderstandingand using genomic data through targeted manipulation of cellular DNA. Ever sincethediscoveryofDNAstructureinthe1950s,researchersandclinicians have been contemplating the possibility of making site-specific changes to thegenomesofcellsandorganisms.Manyoftheearliestapproachestowhat hasbecomeknownasgenomeeditingreliedontheprincipleofsite-specific recognitionofDNAsequences.ThestudyofnaturalDNArepairpathways in bacteria and yeast, as well as the mechanisms of DNA recombination, showedthatcellshaveendogenousmachinerytorepairDNAdouble-strand breaks that would otherwise be lethal. Thus, methods for introducing pre- cisebreaksintheDNAatdesirededitingsiteswererecognizedasavaluable strategy for targeted genomic engineering. Althoughsomeisolatedsuccesseswereachievedusingoligonucleotidesor small molecules to localize DNA-cleaving activities to specific sequences, proteinsthatcouldbeprogrammedtobindandcleaveparticularDNAsites proved more broadly useful. Modular DNA recognition proteins, when coupled to the sequence-independent nuclease domain of the restriction enzymeFokI,couldfunctionassite-specificnucleases.Whendesignedtorec- ognizeachromosomalsequence,suchzinc-fingernucleasesandTALeffector nucleasescanbeeffectiveatinducinggenomicsequencechangesinbothani- mal and plant cells. Difficulties of protein design, synthesis, and validation havelimitedwidespreadadoptionoftheseengineerednucleasesforroutine use,pavingthewayfortheCRISPR/Cas9systeminwhichanaturalprotein with double-stranded DNA-cleaving activity can be programmed with a short RNA sequence to recognize and cut DNA sites of interest. The ease of use, efficiency, and multiplexing capabilities of this technology have enabledrapidadoptionformanydifferentgenomeengineeringapplications. Inthisvolume,weprovidereaderswithacollectionofprotocolsforthe majorprotein-basedgenomeeditingtechniques,withaparticularemphasis xix xx Preface on the more recently developed CRISPR/Cas9 approaches. As these sys- tems are used more widely and for ever-increasing types of projects, we anticipatethatthefacilityofgenomemanipulationforapplicationinhuman health and biotechnology will continue to expand. JENNIFER A. DOUDNA ERIK J. SONTHEIMER
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