Plant Epigenetics and Epigenomics: Methods and Protocols

ISBN-13: 9781071601815 / Angielski / Miękka / 2021 / 272 str.

Charles Spillane; Peter McKeown

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Detection and Analysis of Epigenetic Marks in Plant Genomes

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

Peter C. McKeown and Charles Spillane

2. Approaches to Whole Genome Methylome Analysis in Plants

Xiaodong Yang and Sally A. Mackenzie

3. Understanding DNA Methylation Patterns in Wheat 

Laura-Jayne Gardiner

4. 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, Gianpiero Marconi, and Emidio Albertini

5. 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, and Mieke Van Lijsebettens

6. 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, and Hidetoshi Saze

Part II Epigenetics and Plant Chromatin Structure 

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

Ruben Gutzat and Ortrun Mittelsten Scheid

8. Measurement of Arabidopsis thaliana Nuclear Size and Shape

Kalyanikrishna, Pawel Mikulski, and Daniel Schubert

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

Nan Wang and Chang Liu

10. Chromatin Analysis of Metabolic Gene Clusters in Plants

Ancheng C. Huang and Hans-Wilhelm Nützmann

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

  Pengfei Dong and Silin Zhong

Part III Applications and Novel Insights into Epigenetics and Epigenomics in Plants

12. The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants

Xiaowen Shi, Chen Chen, Hua Yang, Jie Hou, Tieming Ji, Jianlin Cheng, Reiner A. Veitia, and James A. Birchler

13. Identification and Comparison of Imprinted Genes across Plant Species

Colette L. Picard and Mary Gehring

14. Epigenetic Approaches in Non-Model Plants

M. Teresa Boquete, Niels C.A.M. Wagemaker, Philippine Vergeer, Jeannie Mounger, and Christina L. Richards

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

Yang Liu and Yousry A. El-Kassaby

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

Matteo Busconi, Giovanna Soffritti, Marcelino de los Mozos Pascual, and José Antonio Fernandez

17. Plant Epigenetic Stress Memory Induced by Drought: A Physiological and Molecular Perspective

Godwin James and Sara Farrona

18. A Critical Guide for Studies on Epigenetic Inheritance in Plants 

Daniela Ramos Cruz and Claude Becker

Blurb

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.