Plant Gene Regulatory Networks

This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana . Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt
From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants.- Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis.- Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting.- Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation.- Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries.- SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors.- Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems.- Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors.- Characterization of Mediator Complex and its Associated Proteins from Rice.- DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing.- In Situ Hi-C LibraryPreparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale.- Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems.- Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants.- Design of Knowledge Bases for Plant Gene Regulatory Networks.- AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species.- Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development.- Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data.- Computational Approaches to Study Gene Regulatory Networks.- Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation and Prediction.- ODE-Based Modeling of Complex Regulatory Circuits.- Inferring Gene Regulatory Networks in the Arabidopsis Root using a Dynamic Bayesian Network Approach.