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

Preface¿ Table of Contents¿Contributing Authors¿1. From Genes to Networks: Characterizing Gene-Regulatory Interactions in PlantsKerstin Kaufmann and Dijun ChenPart I Experimental Approaches to Study Plant Gene-Regulatory Networks2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis Bennett Thomson, Emmanuelle Graciet, and Frank Wellmer3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting Daniel Slane and Martin Bayer4. Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation On Sun Lau5. Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries Rocío Sánchez-Montesino and Luis Oñate-Sánchez6. SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors Cezary Smaczniak, Gerco C. Angenent and Kerstin Kaufmann7. Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems Sara Díaz-Triviño, Yuchen Long, Ben Scheres, and Ikram Blilou8. Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, and Klaus D. Grasser 9. Characterization of Mediator Complex and its Associated Proteins from Rice Subhasis Samanta and Jitendra Kumar Thakur10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing Sergei A. Filichkin and Molly Megraw11. In Situ Hi-C Library Preparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale Chang Liu12. Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems Levi G. Lowder, Joseph W. Paul III, and Yiping Qi13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants Tom Schreiber and Alain TissierPart II Computational Approaches to Study Plant Gene-Regulatory Networks14. Design of Knowledge Bases for Plant Gene Regulatory Networks Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, and Erich Grotewold15. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species Tak Lee and Insuk Lee16. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development Dijun Chen and Kerstin Kaufmann17. Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data Chun-Ping Yu and Wen-Hsiung Li18. Computational Approaches to Study Gene Regulatory Networks Nooshin Omranian and Zoran Nikoloski19. Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation and Prediction J. Davila-Velderrain, J.C. Martinez-Garcia, and R.E. Alvarez Buylla20. ODE-Based Modeling of Complex Regulatory Circuits Daniel D. Seaton21. Inferring Gene Regulatory Networks in the Arabidopsis Root using a Dynamic Bayesian Network Approach Maria Angels de Luis Balaguer and Rosangela Sozzani