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Plant Chromatin Dynamics

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Marian Bemer

    1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

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  2. Célia Baroux

    1. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1675)

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Table of contents (35 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Profiling of Chromatin States

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming

      • Clara Bourbousse, Moussa Benhamed, Fredy Barneche
      Pages 3-30

    3. Profiling DNA Methylation Using Bisulfite Sequencing (BS-Seq)

      • Yun-Ru Chen, Sheng Yu, Silin Zhong
      Pages 31-43

    4. Bisulfite Sequencing Using Small DNA Amounts

      • Susanne Edelmann, Stefan Scholten
      Pages 45-60

    5. Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana

      • Kamal Kishore, Mattia Pelizzola
      Pages 61-69

    6. A Rapid and Efficient ChIP Protocol to Profile Chromatin Binding Proteins and Epigenetic Modifications in Arabidopsis

      • Bénédicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, Crisanto Gutierrez
      Pages 71-82

    7. Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP)

      • Bénédicte Desvoyes, Joana Sequeira-Mendes, Zaida Vergara, Sofia Madeira, Crisanto Gutierrez
      Pages 83-97

    8. A Method to Identify Nucleolus-Associated Chromatin Domains (NADs)

      • Marie-Christine Carpentier, Ariadna Picart-Picolo, Frédéric Pontvianne
      Pages 99-109

    9. Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins

      • Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
      Pages 111-130

    10. Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry

      • Walid Mahrez, Lars Hennig
      Pages 131-145

    11. Histone H1 Purification and Post-Translational Modification Profiling by High–Resolution Mass Spectrometry

      • Maciej Kotliński, Andrzej Jerzmanowski
      Pages 147-166

    12. Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis

      • Alice Pajoro, Jose M. Muiño, Gerco C. Angenent, Kerstin Kaufmann
      Pages 167-181

    13. Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq

      • Marko Bajic, Kelsey A. Maher, Roger B. Deal
      Pages 183-201

  3. Chromatin Dynamics and Gene Regulation

    1. Front Matter

      Pages 203-203
      Download chapter PDF

    2. Unraveling the Complex Epigenetic Mechanisms that Regulate Gene Activity

      • Marian Bemer
      Pages 205-231

    3. Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture

      • Stefan Grob, Giacomo Cavalli
      Pages 233-246

    4. 3C in Maize and Arabidopsis

      • Blaise Weber, Suraj Jamge, Maike Stam
      Pages 247-270

    5. Profiling Histone Modifications in Synchronized Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics

      • Julia Engelhorn, Frank Wellmer, Cristel C. Carles
      Pages 271-296

    6. De Novo Identification of sRNA Loci and Non-coding RNAs by High-Throughput Sequencing

      • Alice Lunardon, Cristian Forestan, Silvia Farinati, Serena Varotto
      Pages 297-314
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Keywords

About this book

This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. 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.

Authoritative and cutting-edge, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  • Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

Bibliographic Information

  • Book Title: Plant Chromatin Dynamics

  • Book Subtitle: Methods and Protocols

  • Editors: Marian Bemer, Célia Baroux

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7318-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7317-0Published: 20 October 2017

  • Softcover ISBN: 978-1-4939-8451-0Published: 23 August 2018

  • eBook ISBN: 978-1-4939-7318-7Published: 20 October 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 659

  • Number of Illustrations: 24 b/w illustrations, 66 illustrations in colour

  • Topics: Plant Sciences

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