Plant gene regulatory networks : methods and protocols

Author(s)

    • Kaufmann, Kerstin (Plant biologist)
    • Mueller-Roeber, Bernd

Bibliographic Information

Plant gene regulatory networks : methods and protocols

edited by Kerstin Kaufmann, Bernd Mueller-Roeber

(Methods in molecular biology / John M. Walker, series editor, 1629)(Springer protocols)

Humana Press, c2017

  • : hard

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Note

"This Humana Press imprint is published by Springer Nature. The registered company is Springer Science+Business Media LLC"--T.p. verso

Includes bibliographical references and index

Description and Table of Contents

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.

Table of Contents

Preface... Table of Contents... Contributing Authors... 1. From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants Kerstin Kaufmann and Dijun Chen Part I Experimental Approaches to Study Plant Gene-Regulatory Networks 2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis Bennett Thomson, Emmanuelle Graciet, and Frank Wellmer 3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting Daniel Slane and Martin Bayer 4. Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation On Sun Lau 5. Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries Rocio Sanchez-Montesino and Luis Onate-Sanchez 6. SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors Cezary Smaczniak, Gerco C. Angenent and Kerstin Kaufmann 7. Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems Sara Diaz-Trivino, Yuchen Long, Ben Scheres, and Ikram Blilou 8. 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 Thakur 10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing Sergei A. Filichkin and Molly Megraw 11. In Situ Hi-C Library Preparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale Chang Liu 12. Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems Levi G. Lowder, Joseph W. Paul III, and Yiping Qi 13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants Tom Schreiber and Alain Tissier Part II Computational Approaches to Study Plant Gene-Regulatory Networks 14. Design of Knowledge Bases for Plant Gene Regulatory Networks Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, and Erich Grotewold 15. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species Tak Lee and Insuk Lee 16. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development Dijun Chen and Kerstin Kaufmann 17. Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data Chun-Ping Yu and Wen-Hsiung Li 18. Computational Approaches to Study Gene Regulatory Networks Nooshin Omranian and Zoran Nikoloski 19. 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 Buylla 20. ODE-Based Modeling of Complex Regulatory Circuits Daniel D. Seaton 21. Inferring Gene Regulatory Networks in the Arabidopsis Root using a Dynamic Bayesian Network Approach Maria Angels de Luis Balaguer and Rosangela Sozzani

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Details

  • NCID
    BB24766265
  • ISBN
    • 9781493971244
  • Country Code
    us
  • Title Language Code
    eng
  • Text Language Code
    eng
  • Place of Publication
    New York
  • Pages/Volumes
    xi, 350 p.
  • Size
    27 cm
  • Classification
  • Subject Headings
  • Parent Bibliography ID
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