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Plant Gene Regulatory Networks

Methods and Protocols

  • Book
  • © 2023
  • Latest edition

Overview

Editors:
  1. Kerstin Kaufmann

    1. Berlin, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Klaas Vandepoele

    1. Ghent, Belgium

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    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 2698)

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About this book

This second edition details protocols that analyze and explore gene regulatory networks (GRNs). Chapters guide readers through experimental techniques used to study genes and their regulatory interactions in plants, and computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

 

Authoritative and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. 

Keywords

Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types

    • Klaas Vandepoele, Kerstin Kaufmann
    Pages 1-11

  3. Inducible, Tissue-Specific Gene Expression in Arabidopsis Using GR-LhG4-Mediated Trans-Activation

    • Tasnim Zerin, Thomas Greb, Sebastian Wolf
    Pages 13-25

  4. Targeted Activation of Arabidopsis Genes by a Potent CRISPR–Act3.0 System

    • Changtian Pan, Yi** Qi
    Pages 27-40

  5. Single Cell RNA-Sequencing in Arabidopsis Root Tissues

    • Yuji Ke, Max Minne, Thomas Eekhout, Bert De Rybel
    Pages 41-56

  6. Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry

    • Kenneth W. Berendzen, Christopher Grefen, Takuya Sakamoto, Daniel Slane
    Pages 57-73

  7. Untargeted Proteomics and Metabolomics Analysis of Plant Organ Development

    • Venkatesh P. Thirumalaikumar, Alisdair R. Fernie, Aleksandra Skirycz
    Pages 75-85

  8. DamID-seq: A Genome-Wide DNA Methylation Method that Captures Both Transient and Stable TF-DNA Interactions in Plant Cells

    • José M. Alvarez, Will E. Hinckley, Lauriebeth Leonelli, Matthew D. Brooks, Gloria M. Coruzzi
    Pages 87-107

  9. CUT&Tag for Map** In Vivo Protein-DNA Interactions in Plants

    • Weizhi Ouyang, **ngwang Li
    Pages 109-117

  10. Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq

    • Stephanie Hutin, Romain Blanc-Mathieu, Philippe Rieu, François Parcy, Xuelei Lai, Chloe Zubieta
    Pages 119-145

  11. Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq

    • Peilin Chen, Cezary Smaczniak, Johanna Haffner, Jose M. Muino, Kerstin Kaufmann
    Pages 147-161

  12. Immunoprecipitation-Mass Spectrometry (IP-MS) of Protein-Protein Interactions of Nuclear-Localized Plant Proteins

    • Cezary Smaczniak
    Pages 163-181

  13. Map** Active Gene-Associated Chromatin Loops by ChIA-PET in Rice

    • Weizhi Ouyang, **ngwang Li
    Pages 183-194

  14. Building High-Confidence Gene Regulatory Networks by Integrating Validated TF–Target Gene Interactions Using ConnecTF

    • Ji Huang, Manpreet S. Katari, Che-Lun Juang, Gloria M. Coruzzi, Matthew D. Brooks
    Pages 195-220

  15. The ChIP-Hub Resource: Toward plantEncode

    • Yangming Lan, Xue Zhao, Dijun Chen
    Pages 221-231

  16. A Practical Guide to Inferring Multi-Omics Networks in Plant Systems

    • Natalie M. Clark, Bhavna Hurgobin, Dior R. Kelley, Mathew G. Lewsey, Justin W. Walley
    Pages 233-257

  17. Gene Regulatory Network Modeling Using Single-Cell Multi-Omics in Plants

    • Tran Chau, Prakash Timilsena, Song Li
    Pages 259-275

  18. Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information

    • Hadi Nayebi Gavgani, Erich Grotewold, John Gray
    Pages 277-300

  19. Predicting Gene Regulatory Interactions Using Natural Genetic Variation

    • Maura John, Dominik Grimm, Arthur Korte
    Pages 301-322

  20. Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information

    • Nicolás Manosalva Pérez, Klaas Vandepoele
    Pages 323-349
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Editors and Affiliations

  • Berlin, Germany

    Kerstin Kaufmann

  • Ghent, Belgium

    Klaas Vandepoele

Bibliographic Information

  • Book Title: Plant Gene Regulatory Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Kerstin Kaufmann, Klaas Vandepoele

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3354-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3353-3Published: 09 September 2023

  • Softcover ISBN: 978-1-0716-3356-4Due: 10 October 2023

  • eBook ISBN: 978-1-0716-3354-0Published: 08 September 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XII, 382

  • Number of Illustrations: 6 b/w illustrations, 63 illustrations in colour

  • Topics: Plant Sciences, Plant Genetics and Genomics

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