Transcription Factor Regulatory Networks

229 Pages·2022·7.608 MB·English

by  Qi Song, Zhipeng Tao

Methods in
Molecular Biology 2594
1100
11001100
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Qi Song
Zhipeng Tao Editors
Transcription
Factor Regulatory
Networks
M M B
ETHODS IN OLECULAR IO LO GY
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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
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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