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Plant Epigenetics and Epigenomics

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Charles Spillane

    1. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

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  2. Peter McKeown

    1. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2093)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
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  2. Detection and Analysis of Epigenetic Marks in Plant Genomes

    1. Front Matter

      Pages 1-1
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    2. An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena

      • Peter McKeown, Charles Spillane
      Pages 3-13

    3. Approaches to Whole-Genome Methylome Analysis in Plants

      • Xiaodong Yang, Sally A. Mackenzie
      Pages 15-31

    4. Understanding DNA Methylation Patterns in Wheat

      • Laura-Jayne Gardiner
      Pages 33-46

    5. MCSeEd (Methylation Context Sensitive Enzyme ddRAD): A New Method to Analyze DNA Methylation

      • Marco Di Marsico, Elisa Cerruti, Cinzia Comino, Andrea Porceddu, Alberto Acquadro, Stefano Capomaccio et al.
      Pages 47-64

    6. Plant-RRBS: DNA Methylome Profiling Adjusted to Plant Genomes, Utilizing Efficient Endonuclease Combinations, for Multi-Sample Studies

      • Martin Schmidt, Magdalena Woloszynska, Michiel Van Bel, Frederik Coppens, Mieke Van Lijsebettens
      Pages 65-80

    7. Rice Histone Propionylation and Generation of Chemically Derivatized Synthetic H3 and H4 Peptides for Identification of Acetylation Sites and Quantification

      • Nino A. Espinas, Alejandro Villar-Briones, Michael C. Roy, Hidetoshi Saze
      Pages 81-92

  3. Epigenetics and Plant Chromatin Structure

    1. Front Matter

      Pages 93-93
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    2. Preparing Chromatin and RNA from Rare Cell Types with Fluorescence-Activated Nuclear Sorting (FANS)

      • Ruben Gutzat, Ortrun Mittelsten Scheid
      Pages 95-105

    3. Measurement of Arabidopsis thaliana Nuclear Size and Shape

      • Kalyanikrishna, Pawel Mikulski, Daniel Schubert
      Pages 107-113

    4. Study of Cell-Type-Specific Chromatin Organization: In Situ Hi-C Library Preparation for Low-Input Plant Materials

      • Nan Wang, Chang Liu
      Pages 115-127

    5. Chromatin Analysis of Metabolic Gene Clusters in Plants

      • Ancheng C. Huang, Hans-Wilhelm Nützmann
      Pages 129-146

    6. Characterization of Plant 3D Chromatin Architecture, In Situ Hi-C Library Preparation, and Data Analysis

      • Pengfei Dong, Silin Zhong
      Pages 147-157

  4. Applications and Novel Insights into Epigenetics and Epigenomics in Plants

    1. Front Matter

      Pages 159-159
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    2. The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants

      • Xiaowen Shi, Chen Chen, Hua Yang, Jie Hou, Tieming Ji, Jianlin Cheng et al.
      Pages 161-171

    3. Identification and Comparison of Imprinted Genes Across Plant Species

      • Colette L. Picard, Mary Gehring
      Pages 173-201

    4. Epigenetic Approaches in Non-Model Plants

      • M. Teresa Boquete, Niels C. A. M. Wagemaker, Philippine Vergeer, Jeannie Mounger, Christina L. Richards
      Pages 203-215

    5. Techniques for Small Non-Coding RNA Analysis in Seeds of Forest Tree Species

      • Yang Liu, Yousry A. El-Kassaby
      Pages 217-225

    6. Epigenetic Barcodes for Detection of Adulterated Plants and Plant-Derived Products

      • Matteo Busconi, Giovanna Soffritti, Marcelino De Los Mozos Pascual, José Antonio Fernandez
      Pages 227-242
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Keywords

About this book

This second edition volume expands on the previous edition with a look at the latest techniques in plant epigenetics and epigenomic research. Chapters in this book cover topics such as whole genome methylome analysis; analysis of DNA methylation; chromatin analysis of metabolic gene clusters in plants; plant epigenetic stress memory induced by drought; small non-coding RNA analysis in seeds of forest tree species; and a discussion on epigenetics inheritance in plants. 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.
 
Cutting-edge and comprehensive, Plant Epigenetics and Epigenomics: Methods and Protocols, Second Edition is a valuable resource for both novice and expert researchers, and aims to advance this field of study by paving the way for integrating epigenetic mechanisms into models of plant function during development and evolution. 


Editors and Affiliations

  • Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Charles Spillane, Peter McKeown

Bibliographic Information

  • Book Title: Plant Epigenetics and Epigenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Charles Spillane, Peter McKeown

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0179-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0178-5Published: 23 February 2020

  • Softcover ISBN: 978-1-0716-0181-5Published: 26 August 2021

  • eBook ISBN: 978-1-0716-0179-2Published: 22 February 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 272

  • Number of Illustrations: 12 b/w illustrations, 39 illustrations in colour

  • Topics: Plant Genetics and Genomics

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