Skip to main content
SpringerLink
Log in

Plant Gene Regulatory Networks

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Kerstin Kaufmann

    1. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Bernd Mueller-Roeber

    1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1629)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants

    • Kerstin Kaufmann, Dijun Chen
    Pages 1-11

  3. Experimental Approaches to Study Plant Gene-Regulatory Networks

    1. Front Matter

      Pages 13-13
      Download chapter PDF

    2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis

      • Bennett Thomson, Emmanuelle Graciet, Frank Wellmer
      Pages 15-25

    3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting

      • Daniel Slane, Martin Bayer
      Pages 27-35

    4. Characterization of Cell-Type-Specific DNA Binding Sites of Plant Transcription Factors Using Chromatin Immunoprecipitation

      • On Sun Lau
      Pages 37-45

    5. Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries

      • Rocío Sánchez-Montesino, Luis Oñate-Sánchez
      Pages 47-65

    6. SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors

      • Cezary Smaczniak, Gerco C. Angenent, Kerstin Kaufmann
      Pages 67-82

    7. Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems

      • Sara Díaz-Triviño, Yuchen Long, Ben Scheres, Ikram Blilou
      Pages 83-103

    8. Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors

      • Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, Klaus D. Grasser
      Pages 105-122

    9. Characterization of Mediator Complex and its Associated Proteins from Rice

      • Subhasis Samanta, Jitendra Kumar Thakur
      Pages 123-140

    10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing

      • Sergei A. Filichkin, Molly Megraw
      Pages 141-154

    11. In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale

      • Chang Liu
      Pages 155-166

    12. Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems

      • Levi G. Lowder, Joseph W. Paul III, Yiping Qi
      Pages 167-184

    13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants

      • Tom Schreiber, Alain Tissier
      Pages 185-204

  4. Computational Approaches to Study Plant Gene-Regulatory Networks

    1. Front Matter

      Pages 205-205
      Download chapter PDF

    2. Design of Knowledge Bases for Plant Gene Regulatory Networks

      • Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, Erich Grotewold
      Pages 207-223

    3. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species

      • Tak Lee, Insuk Lee
      Pages 225-238

    4. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development

      • Dijun Chen, Kerstin Kaufmann
      Pages 239-269

    5. Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data

      • Chun-Ping Yu, Wen-Hsiung Li
      Pages 271-282
Back to top

Keywords

About this book

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.

Editors and Affiliations

  • Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Kerstin Kaufmann

  • Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Bernd Mueller-Roeber

Bibliographic Information

  • Book Title: Plant Gene Regulatory Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Kerstin Kaufmann, Bernd Mueller-Roeber

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7125-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7124-4Published: 17 June 2017

  • Softcover ISBN: 978-1-4939-8392-6Published: 08 August 2018

  • eBook ISBN: 978-1-4939-7125-1Published: 15 June 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 350

  • Number of Illustrations: 6 b/w illustrations, 51 illustrations in colour

  • Topics: Plant Sciences

Publish with us

Policies and ethics

Back to top

Search

Navigation