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Methods in Molecular Biology 2594 1100 11001100 11001111001100.... Qi Song Zhipeng Tao Editors Transcription Factor Regulatory Networks 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 biomedical protocol publishing. Each protocol is provided in readily-reproducible step-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. Transcription Factor Regulatory Networks Edited by Qi Song Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA Zhipeng Tao Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA Editors QiSong ZhipengTao ComputationalBiologyDepartment CutaneousBiologyResearchCenter CarnegieMellonUniversity MassachusettsGeneralHospital,Harvard Pittsburgh,PA,USA MedicalSchool Charlestown,MA,USA ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2814-0 ISBN978-1-0716-2815-7 (eBook) https://doi.org/10.1007/978-1-0716-2815-7 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2023 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,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface Transcriptionfactors(TFs)arethemajormodulatorsofgeneregulationinlivingcells.TFs regulate gene expression by preferentially binding to specific genomic regions on the chromatin. Systematic approaches are needed to characterize regulatory events at genomic scale. In recent years, a myriad of experimental and computational approaches have been developed to investigate complex associations between TFs and targeted genomic regions. This book covers various state-of-the-art techniques regarding the TFs-genes associations, with a focus on providing methodological and practical references for researchers. In this volume, we aim to cover diverse protocols and summaries of TFs including screening of TF-DNA interactions, detection of open chromatin regions, identification of epigenetic regulations, engineering TFs with genome editing tools, detection of transcriptional activ- ities, and computational analysis of TF networks. Additionally, several chapters focused on presenting a comprehensive review of functions and druggabilities of TFs in biomedical research, such as cell fate reprogramming and development of molecular drugs. With the emerging interests of single-cell techniques, several chapters focus on applying single-cell- based approaches to promote thestudies of TFs.We arehoping that this bookwillbenefit readerswhoareinterestedinusingstate-of-the-arttechniquestostudyTFs,andthisvolume will serve as a step-by-step protocol for performing experiments and troubleshooting in theirstudies. Pittsburgh,PA,USA QiSong Charlestown,MA,USA ZhipengTao v Contents Preface ..................................................................... v Contributors................................................................. ix 1 TheTARGETSystem:RapidIdentificationofDirectTargets ofTranscriptionFactorsbyGeneRegulationinPlantCells.... ....... ........ 1 MatthewD.Brooks,KelseyM.Reed,GabrielKrouk, GloriaM.Coruzzi,andBastiaanO.R.Bargmann 2 TheMethodofScreeningandIdentificationofTranscription FactorinKlebsiella.. ....... ........ ....... ....... ........ ....... ........ 13 QiangWu,Gao-QiangLiu,Jiang-ShanMa,andQiangLi 3 Genome-WideIdentificationofOpenChromatininPlants UsingMH-Seq..... ....... ........ ....... ....... ........ .. ..... ...... .. 29 AicenZhang,XinxuLi,HainanZhao,JimingJiang,andWenliZhang 4 Post-bisulfiteAdaptorTaggingwithaHighlyEfficientSingle-Stranded DNALigationTechnique........... ....... ....... ........ ....... ........ 45 FumihitoMiuraandTakashiIto 5 PerturbationofGeneRegulationbyGenomeEditing........ ....... ........ 59 NanCherYeoandGeorgeM.Church 6 AnalysisofNeutrophilMorphologyandFunctionUnderGenetic PerturbationofTranscriptionFactorsInVitro....... ........ ....... ........ 69 JuliaSalafranca,ZhichaoAi,LihuiWang, IrinaA.Udalova,andErinkevanGrinsven 7 DetectionofTP53MutationinAcuteMyeloidLeukemia byRT-PCR-BasedSangerSequencing.. ..... ....... ........ ....... ........ 87 EmilyR.Novak,AnaghaDeshpande,DarrenFinlay,JamesR.Mason, AniruddhaJ.Deshpande,PeterD.Adams,andShaLi 8 AssessingtheActivityofTranscriptionFactorFoxO1......... ....... ........ 97 LiminShi,ZhipengTao,andZhiyongCheng 9 TargetingTranscriptionFactorsinCancer:From“Undruggable” to“Druggable”..... ....... ........ ....... ....... ........ ....... ........ 107 ZhipengTaoandXuWu 10 ASurveyofTranscriptionFactorsinCellFateControl ....... ....... ........ 133 EmalLesha,HaydyGeorge,MarkM.Zaki,CoryJ.Smith, ParastooKhoshakhlagh,andAlexH.M.Ng 11 Single-CellmRNA-SeqofInVitro-DerivedHumanNeurons UsingSmart-Seq2 ......... ........ ....... ....... ........ ....... ........ 143 ChristophSchweingruber,JikNijssen,JulioAguilaBenitez, andEvaHedlund vii viii Contents 12 ComputationalAnalysisofSingle-CellRNA-SeqData........ ....... ........ 165 ByungjinHwang 13 DatabaseforPlantTranscriptionFactorBindingSites........ ....... ........ 173 Wen-ChiChangandChi-NgaChow 14 MicroRNARegulatoryNetworkAnalysisUsingmiRNet2.0......... ........ 185 LeChangandJianguoXia 15 ModelingPlantTranscriptionFactorNetworksUsingConSReg...... ........ 205 QiSongandSongLi 16 IdentificationofPlantCo-regulatoryModulesUsingCoReg......... ........ 217 QiSongandSongLi Index ...................................................................... 225 Contributors PETERD.ADAMS • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla,CA,USA ZHICHAO AI • KennedyInstituteofRheumatology,UniversityofOxford,Oxford,UK BASTIAANO.R.BARGMANN • SchoolofPlantandEnvironmentalSciences,Virginia PolytechnicInstituteandStateUniversity,Blacksburg,VA,USA JULIO AGUILABENITEZ • DepartmentofNeuroscience,KarolinskaInstitutet,Stockholm, Sweden MATTHEWD.BROOKS • Center forGenomicsandSystemsBiology,DepartmentofBiology, NewYorkUniversity,NewYork,NY,USA;USDAARSGlobalChangeandPhotosynthesis ResearchUnit,Urbana,IL,USA LECHANG • DepartmentofHumanGenetics,McGillUniversity,Montreal,QC,Canada WEN-CHICHANG • InstituteofTropicalPlantSciencesandMicrobiology,NationalCheng KungUniversity,Tainan,Taiwan ZHIYONGCHENG • FoodScienceandHumanNutritionDepartment,UniversityofFlorida, Gainesville,FL,USA;DepartmentofHumanNutrition,Foods,andExercise,Virginia Tech,Blacksburg,VA,USA CHI-NGACHOW • InstituteofTropicalPlantSciencesandMicrobiology,NationalCheng KungUniversity,Tainan,Taiwan GEORGEM.CHURCH • WyssInstituteforBiologicallyInspiredEngineering,Harvard University,Cambridge,MA,USA;DepartmentofGenetics,HarvardMedicalSchool, Boston,MA,USA GLORIAM.CORUZZI • CenterforGenomicsandSystemsBiology,DepartmentofBiology,New YorkUniversity,NewYork,NY,USA ANAGHADESHPANDE • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla,CA, USA ANIRUDDHAJ.DESHPANDE • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla, CA,USA DARRENFINLAY • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla,CA,USA HAYDYGEORGE • GCTherapeuticsInc.,Cambridge,MA,USA;SchoolofMedicine,St. George’sUniversity,Grenada,WestIndies EVAHEDLUND • DepartmentforBiochemistryandBiophysics,StockholmUniversity, Stockholm,Sweden;DepartmentofCellandMolecularBiology,KarolinskaInstitutet, Stockholm,Sweden BYUNGJINHWANG • SeveranceBiomedicalScienceInstitute,YonseiUniversityCollegeof Medicine,Seoul,SouthKorea TAKASHIITO • DepartmentofBiochemistry,KyushuUniversityGraduateSchoolofMedical Sciences,Fukuoka,Japan JIMING JIANG • DepartmentofPlantBiology,MichiganStateUniversity,EastLansing,MI, USA;DepartmentofHorticulture,MichiganStateUniversity,EastLansing,MI,USA PARASTOOKHOSHAKHLAGH • GCTherapeuticsInc.,Cambridge,MA,USA GABRIEL KROUK • BPMP,UnivMontpellier,CNRS,INRA,SupAgro,Montpellier,France EMALLESHA • GCTherapeuticsInc.,Cambridge,MA,USA;DepartmentofNeurosurgery, UniversityofTennesseeHealthScienceCenter,Memphis,TN,USA ix x Contributors QIANGLI • HunanProvincialKeyLaboratoryofForestryBiotechnology&International CooperationBaseofScienceandTechnologyInnovationonForestResourceBiotechnology, CentralSouthUniversityofForestryandTechnology,Changsha,China;MicrobialVariety CreationCenter,NationalLaboratoryofYuelushanSeedIndustry,Changsha,China SHALI • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla,CA,USA SONG LI • SchoolofPlantandEnvironmentalSciences,VirginiaPolytechnicInstituteand StateUniversity,Blacksburg,VA,USA XINXU LI • StateKeyLaboratoryforCropGeneticsandGermplasmEnhancement,JCIC- MCP,CIC-MCP,NanjingAgriculturalUniversity,Nanjing,Jiangsu,People’sRepublic ofChina GAO-QIANGLIU • HunanProvincialKeyLaboratoryofForestryBiotechnology& InternationalCooperationBaseofScienceandTechnologyInnovationonForestResource Biotechnology,CentralSouthUniversityofForestryandTechnology,Changsha,China; MicrobialVarietyCreationCenter,NationalLaboratoryofYuelushanSeedIndustry, Changsha,China JIANG-SHANMA • HunanProvincialKeyLaboratoryofForestryBiotechnology& InternationalCooperationBaseofScienceandTechnologyInnovationonForestResource Biotechnology,CentralSouthUniversityofForestryandTechnology,Changsha,China; MicrobialVarietyCreationCenter,NationalLaboratoryofYuelushanSeedIndustry, Changsha,China JAMESR.MASON • ScrippsMDAndersonCancerCenter,LaJolla,CA,USA FUMIHITO MIURA • DepartmentofBiochemistry,KyushuUniversityGraduateSchoolof MedicalSciences,Fukuoka,Japan ALEXH.M.NG • GCTherapeuticsInc.,Cambridge,MA,USA JIKNIJSSEN • DepartmentofCellandMolecularBiology,KarolinskaInstitutet,Stockholm, Sweden EMILYR.NOVAK • SanfordBurnhamPrebysMedicalDiscoveryInstitute,LaJolla,CA,USA KELSEYM.REED • SchoolofPlantandEnvironmentalSciences,VirginiaPolytechnic InstituteandStateUniversity,Blacksburg,VA,USA JULIASALAFRANCA • KennedyInstituteofRheumatology,UniversityofOxford,Oxford,UK CHRISTOPHSCHWEINGRUBER • DepartmentforBiochemistryandBiophysics,Stockholm University,Stockholm,Sweden;DepartmentofCellandMolecularBiology,Karolinska Institutet,Stockholm,Sweden LIMIN SHI • FoodScienceandHumanNutritionDepartment,UniversityofFlorida, Gainesville,FL,USA CORY J.SMITH • GCTherapeuticsInc.,Cambridge,MA,USA QISONG • ComputationalBiologyDepartment,CarnegieMellonUniversity,Pittsburgh, PA,USA;ComputationalBiologyDepartment,CarnegieMellonUniversity,Pittsburgh, PA,USA ZHIPENG TAO • DepartmentofHumanNutrition,Foods,andExercise,VirginiaTech, Blacksburg,VA,USA;CutaneousBiologyResearchCenter,MassachusettsGeneralHospital, HarvardMedicalSchool,Charlestown,MA,USA IRINAA.UDALOVA • KennedyInstituteofRheumatology,UniversityofOxford,Oxford,UK ERINKEVANGRINSVEN • KennedyInstituteofRheumatology,UniversityofOxford,Oxford, UK LIHUI WANG • KennedyInstituteofRheumatology,UniversityofOxford,Oxford,UK QIANGWU • CollegeofFoodandChemicalEngineering,ShaoyangUniversity,Shaoyang, China;HunanProvincialKeyLaboratoryofForestryBiotechnology&International