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Full Description
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.
Contents
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.
