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
- 2.1 Affinity-Purification of TEFs Expressed in Cultured Cells
- 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 Immuno precipitation (IP)
- 3.2.4 Washing and Elution
- 3.2.5 DNA Extraction and Signal Quantification
- 3.1 Affinity-Purification of TEFs Expressed in Cultured Cells
- 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 Immuno precipitation 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 Immuno precipitation 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
- 3.1 Construction of dTALEs
- 4 Notes
- References
- 1 Introduction
- Chapter 2: Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
- 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
- 3.1 Data Scope Definition
- 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])
- 3.1 Correlation- Based Approaches
- 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
- Chapter 14: Design of Knowledge Bases for Plant Gene Regulatory Networks
- Index
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