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标题:Plant Gene Regulatory Networks
时间:2020-05-22 23:29:22
DOI:10.1007/978-1-4939-7125-1
大小:7640 kb
页数:349 PAGES
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目录:
  • Preface
  • Contents
  • Contributors
  • Chapter 1: From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants
    • 1 Introduction
    • 2 Experimental Approaches to Analyze GRNs in Plants
    • 3 Data Analysis and Mathematical Modeling
    • 4 Conclusions
    • References
  • Part I: Experimental Approaches to Study Plant Gene-Regulatory Networks
    • Chapter 2: Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
      • 1 Introduction
      • 2 Materials
        • 2.1 Plant Materials and Growth
        • 2.2 Agrobacterium-Mediated Plant Transformation
        • 2.3 Induction of Flower Formation in the Floral Induction System
        • 2.4 Induction of the Ethanol-­Sensitive AlcApro/AlcR Systems
        • 2.5 Tissue Collection AP1pro:AP1-GR Inflorescences
      • 3 Methods
        • 3.1 Generation of amiRNAs for Use in Inducible Promoter Systems
        • 3.2 Agrobacterium-­Mediated Super-­Transformation of AP1pro:AP1-GR ap1-1 cal-1
        • 3.3 Ethanol-­Mediated Induction of amiRNAs
        • 3.4 Growth and Treatment of Dexamethasone-­Inducible amiRNA Plants
      • 4 Notes
      • References
    • Chapter 3: Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
      • 1 Introduction
      • 2 Materials
        • 2.1 Tissue Collection and Homogenization
        • 2.2 Nuclear Extraction
        • 2.3 FANS
        • 2.4 RNA Extraction
        • 2.5 RNA Amplification and Biotinylation
      • 3 Methods
        • 3.1 Tissue Collection and Fixation
        • 3.2 Nuclear Extraction
        • 3.3 FANS
        • 3.4 RNA Extraction and Amplification
        • 3.5 RNA Amplification, Biotinylation, and Microarray Hybridization
      • 4 Notes
      • References
    • Chapter 4: Characterization of Cell-Type-Specific DNA Binding Sites of Plant Transcription Factors Using Chromatin Immunoprecipitation
      • 1 Introduction
      • 2 Materials
        • 2.1 Reagents
        • 2.2 Buffers
        • 2.3 Equipment
      • 3 Methods
        • 3.1 Harvesting and Formaldehyde Cross-Linking of Plant Materials
        • 3.2 Isolation and Sonication of Chromatin
        • 3.3 Immunopreci­pitation of Chromatin
        • 3.4 Reverse Cross-­Linking and Purification of ChIPed DNA
      • 4 Notes
      • References
    • Chapter 5: Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries
      • 1 Introduction
      • 2 Materials
        • 2.1 Media and Reagents
        • 2.2 Disposables and Small Equipment (See Fig. 2)
      • 3 Methods
        • 3.1 Preparation of DNA and Protein Baits for Y1H and Y2H Screenings
        • 3.2 Yeast Transformation (Modified from [36])
        • 3.3 Titrating Bait Autoactivation of the HIS3 Reporter Gene Before the Screening (See Note 15 and Fig. 3a)
        • 3.4 Screening Yeast Arrayed Libraries (See Note 17 and Fig. 3b)
        • 3.5 Confirming Positive Interactions and Quantifying Strength
        • 3.6 Making Yeast Glycerol Stocks for Long Term Storage
      • 4 Notes
      • References
    • Chapter 6: SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors
      • 1 Introduction
      • 2 Materials
        • 2.1 Double-Stranded DNA Library Preparation
        • 2.2 Coating Magnetic Beads with Antibodies
        • 2.3 Protein (Protein Complex) In Vitro Synthesis
        • 2.4 First Round (R1) of SELEX
        • 2.5 PCR Amplification of the Selected DNA Sequences
        • 2.6 Validation of SELEX by Electrophoretic Mobility Shift Assay (EMSA)
        • 2.7 High-Throughput Sequencing of the SELEX Libraries
        • 2.8 Sanger Sequencing of the SELEX Libraries
      • 3 Methods
        • 3.1 Double-Stranded DNA Library Preparation
        • 3.2 Coating Magnetic Beads with Antibodies
        • 3.3 Protein (Protein Complex) In Vitro Synthesis
        • 3.4 First Round (R1) of SELEX
        • 3.5 PCR Amplification of the Selected DNA Sequences
        • 3.6 Subsequent Rounds (Rx) of SELEX
        • 3.7 Validation of SELEX by Electrophoretic Mobility Shift Assay (EMSA)
        • 3.8 High-Throughput Sequencing of the SELEX Libraries
        • 3.9 Sanger Sequencing of the SELEX Libraries
      • 4 Notes
      • References
    • Chapter 7: Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
      • 1 Introduction
      • 2 Materials
        • 2.1 Arabidopsis Mesophyll Protoplasts Transfection
        • 2.2 Agroinfiltration of Nicotiana Benthamiana Leaves
        • 2.3 HeLa Cell Transfection
        • 2.4 Luciferase Activity Measurement and Data Analysis
      • 3 Methods
        • 3.1 Transfection of Arabidopsis Mesophyll Protoplasts
        • 3.2 Agroinfiltration of Nicotiana Leaves
        • 3.3 HeLa Cell Transfection
        • 3.4 Luciferase Activity Measurement and Data Analysis
      • 4 Notes
      • References
    • Chapter 8: Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
      • 1 Introduction
      • 2 Materials
        • 2.1 Affinity-­Purification of TEFs Expressed in Cultured Cells
          • 2.1.1 Transformation and Upscaling of Arabidopsis Cell Culture
          • 2.1.2 Coupling of Rabbit IgGs to Magnetic Beads
          • 2.1.3 Affinity Purification of Protein Complexes
          • 2.1.4 Protein Precipitation by Acetone
          • 2.1.5 Separation of Purified Proteins by SDS-PAGE Electrophoresis
          • 2.1.6 In-Gel Digestion of Purified Proteins by Trypsin
          • 2.1.7 Tandem Mass Spectrometry and Data Analysis
        • 2.2 Chromatin Immunoprecipitation (ChIP) of Transcript Elongation Factors
      • 3 Methods
        • 3.1 Affinity-­Purification of TEFs Expressed in Cultured Cells
          • 3.1.1 Transformation and Upscaling of Arabidopsis Cell Culture
          • 3.1.2 Coupling of Rabbit IgGs to Magnetic Beads
          • 3.1.3 Affinity Purification of Protein Complexes
          • 3.1.4 Concentration of Proteins by Acetone Precipitation
          • 3.1.5 Separation of Purified Proteins by SDS-PAGE Electrophoresis
          • 3.1.6 In-Gel Digestion of Purified Proteins by Trypsin
          • 3.1.7 Identification of Purified Proteins by Tandem Mass Spectrometry
          • 3.1.8 Analysis of MS Data
        • 3.2 Chromatin Immunoprecipitation (ChIP) of Transcript Elongation Factors
          • 3.2.1 Plant Material
          • 3.2.2 Chromatin Preparation
          • 3.2.3 Immunoprecipitation (IP)
          • 3.2.4 Washing and Elution
          • 3.2.5 DNA Extraction and Signal Quantification
      • 4 Notes
      • References
    • Chapter 9: Characterization of Mediator Complex and its Associated Proteins from Rice
      • 1 Introduction
      • 2 Materials
        • 2.1 Generation of Antibodies against Conserved Mediator Subunits
        • 2.2 Generation of Rice Callus
        • 2.3 Preparation of Whole Cell Protein Extract from Rice Calli
        • 2.4 Enrichment of Mediator Complex Containing Fraction
          • 2.4.1 Ammonium Sulfate Precipitation
          • 2.4.2 Gel Filtration Chromatography
          • 2.4.3 Immunoprecipitation Using Custom-Made Antibodies
          • 2.4.4 Pulldown of the Mediator Complex by Using HaloLink Resin
        • 2.5 Identification of Mediator Complex Components by Mass-Spectrometry
      • 3 Methods
        • 3.1 Generation of Antibodies against Conserved Mediator Subunits
        • 3.2 Generation of Rice Callus
        • 3.3 Preparation of Whole Cell Protein Extract from Rice Calli
        • 3.4 Enrichment of Mediator Complex Containing Fraction
          • 3.4.1 Ammonium Sulfate Precipitation
          • 3.4.2 Gel Filtration Chromatography
          • 3.4.3 Immunoprecipitation Using Custom-Made Antibodies
          • 3.4.4 Pulldown of the Mediator Complex Using HaloLink Resin
        • 3.5 Identification of the Mediator Complex Components by Mass-Spectrometry
      • 4 Notes
      • References
    • Chapter 10: DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
      • 1 Introduction
      • 2 Materials
        • 2.1 Plant Growth Conditions
        • 2.2 Nuclei Isolation
        • 2.3 DNAse I Digestion and DNA Ends Polishing
        • 2.4 DNase-Seq Library Construction
      • 3 Methods
        • 3.1 Preparation of Plant Material
        • 3.2 Isolation of Nuclei
        • 3.3 DNase I Digestion and DNA Ends Polishing
        • 3.4 DNase-Seq Library Construction
        • 3.5 Genome Alignment and Mapping of DNase I Hypersensitive Sites
      • 4 Notes
      • References
    • Chapter 11: In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-­Wide Scale
      • 1 Introduction
      • 2 Materials
        • 2.1 Tissue Fixation
        • 2.2 Nuclei Isolation
        • 2.3 Chromatin Digestion, Ligation, and DNA Purification
        • 2.4 DNA Manipulation and Library Amplification
      • 3 Methods
        • 3.1 Tissue Fixation
        • 3.2 Nuclei Isolation
        • 3.3 Chromatin Digestion, Ligation, and DNA Purification
        • 3.4 DNA Manipulation and Library Amplification
      • 4 Notes
      • References
    • Chapter 12: Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems
      • 1 Introduction
      • 2 Materials
      • 3 Methods
        • 3.1 gRNA Design, Cloning, and Assembly to T-DNA Destination Vector
        • 3.2 RNA Extraction
        • 3.3 cDNA Synthesis and qRT-PCR
      • 4 Notes
      • References
    • Chapter 13: Generation of dTALEs and Libraries of Synthetic TALE-­Activated Promoters for Engineering of Gene Regulatory Networks in Plants
      • 1 Introduction
        • 1.1 TALEs as Programmable Transcriptional Activators in Plants
        • 1.2 Rules for the Design of dTALEs
        • 1.3 Properties of Synthetic TALE-­Activated Promoters
      • 2 Materials
        • 2.1 Oligonucleotides
        • 2.2 Enzymes
        • 2.3 Kits
        • 2.4 Solutions
        • 2.5 Antibiotics and Selection Additives
      • 3 Methods
        • 3.1 Construction of dTALEs
          • 3.1.1 Cloning of Repeat Arrays (Days 1 and 2)
          • 3.1.2 Construction of dTALE Coding Sequence (Days 3 and 4)
          • 3.1.3 Construction of dTALE Transcriptional Units
        • 3.2 Construction of STAPs
          • 3.2.1 Amplification and Cloning of STAP GG Modules (Day 1–4)
          • 3.2.2 Cloning of STAPs into Transcriptional Units (Day 4)
        • 3.3 Assays of STAPs
      • 4 Notes
      • References
  • Part II: Computational Approaches to Study Plant Gene-Regulatory Networks
    • Chapter 14: Design of Knowledge Bases for Plant Gene Regulatory Networks
      • 1 Introduction
      • 2 Materials
        • 2.1 Hardware and Software
        • 2.2 Expertise
      • 3 Methods
        • 3.1 Data Scope Definition
          • 3.1.1 Identification and Classification of Trans-Acting Factors
          • 3.1.2 Identification of TF-Target Gene Interactions
          • 3.1.3 Mapping of Transcription Start Sites
          • 3.1.4 Prediction of TF Binding Sites (TFBSs)
          • 3.1.5 Manual Curation
        • 3.2 Schema Design
          • 3.2.1 Develop the Schema
          • 3.2.2 Create the Schema
        • 3.3 Implement the Database
          • 3.3.1 Create Data Definition Language Statements (DDL)
          • 3.3.2 Populate the Database
        • 3.4 User Interface Development
          • 3.4.1 Web Server Setup
          • 3.4.2 Create the Web Applications
          • 3.4.3 Develop Landing Page
          • 3.4.4 Develop Queries and the Query Interface
          • 3.4.5 Implement Query Interface: Example
          • 3.4.6 Implement Search Features
      • 4 Notes
      • References
    • Chapter 15: AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
      • 1 Introduction
      • 2 Materials
        • 2.1 Website
        • 2.2 Input Genes for Network Searches
      • 3 Methods
        • 3.1 Find New Members of a Pathway
        • 3.2 Infer Function from Network Neighbors
        • 3.3 Other Useful Features of AraNet
      • 4 Notes
      • References
    • Chapter 16: Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
      • 1 Introduction
      • 2 Materials
        • 2.1 Workspace
        • 2.2 Software Installation
        • 2.3 Sample Data
        • 2.4 Genome Sequence and Annotation
      • 3 Methods
        • 3.1 Getting Started
        • 3.2 Initial Data Quality Inspection
        • 3.3 Sequence Alignment
        • 3.4 Filtering and Quality Metrics
        • 3.5 Data Visualization
        • 3.6 Calling Peak Using MACS2
        • 3.7 IDR: Reproducibility Assessment
        • 3.8 Peak Annotation
        • 3.9 Target Gene Analysis and Gene Regulatory Networks
      • 4 Notes
      • References
    • Chapter 17: Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data
      • 1 Introduction
      • 2 Materials
        • 2.1 Time-Course Transcriptomes
        • 2.2 Bioinformatics Resources for Predicting TFBSs and Their Cognate TFs
      • 3 Methods
        • 3.1 Selection of Co-expressed Genes in a Functional Category
        • 3.2 Motif Discovery and Conservation Test
        • 3.3 Identifying the Cognate TF of a TFBS
      • 4 Notes
      • References
    • Chapter 18: Computational Approaches to Study Gene Regulatory Networks
      • 1 Introduction
      • 2 Materials
        • 2.1 Gene Expression Data
        • 2.2 Computational Requirements
      • 3 Methods
        • 3.1 Correlation-Based Approaches
          • 3.1.1 Theoretical Considerations
          • 3.1.2 Application of a Graphical Gaussian Model (R Package GeneNet [16])
        • 3.2 Information-Theoretic-Based Approaches
          • 3.2.1 Theoretical Considerations
          • 3.2.2 Application of ARACNE (R Package Minet [23])
          • 3.2.3 Application of CLR (R Package Minet [23])
        • 3.3 Bayesian Network Approaches
          • 3.3.1 Theoretical Considerations
          • 3.3.2 Categorical Bayesian Network Inference (R Package Catnet [40])
        • 3.4 Regression-Based Approaches
          • 3.4.1 Theoretical Considerations
          • 3.4.2 Fused LASSO (R Package Lqa [48])
      • 4 Notes
      • References
    • Chapter 19: Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction
      • 1 Introduction
      • 2 Materials
        • 2.1 Data
        • 2.2 Software
      • 3 Methods
        • 3.1 Definitions
        • 3.2 Boolean GRN Modeling
          • 3.2.1 Building a Boolean GRN Model from Scratch
          • 3.2.2 Boolean GRN Dynamical Analysis
      • 4 Notes
      • References
    • Chapter 20: ODE-Based Modeling of Complex Regulatory Circuits
      • 1 Introduction
      • 2 Materials
      • 3 Methods
        • 3.1 Evaluating the Suitability of ODE Modeling
        • 3.2 Representing Biochemistry with ODEs
        • 3.3 Simulating the Model
          • 3.3.1 Describe the Model Dynamics
          • 3.3.2 Set Up Simulation Conditions
          • 3.3.3 Run Simulations
          • 3.3.4 Plot Simulation Results
        • 3.4 Selection of Experimental Data
        • 3.5 Parameter Optimization
          • 3.5.1 Initial Parameter Values
          • 3.5.2 Describe Objective Function
          • 3.5.3 Optimize Parameters
          • 3.5.4 Review Results
        • 3.6 Understanding Model Behavior
          • 3.6.1 Parameter Sensitivity
          • 3.6.2 Making Predictions
        • 3.7 Iterative Model Development
      • 4 Notes
      • References
    • Chapter 21: Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach
      • 1 Introduction
      • 2 Materials
      • 3 Methods
        • 3.1 Definitions
        • 3.2 DBN Inference
        • 3.3 Practical Implementation of the Method Through an Example: Application to an Arabidopsis Root Dataset
          • 3.3.1 Computation of the GRN
          • 3.3.2 Validation
      • 4 Notes
      • References
  • Index

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