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Plant Epigenetics

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Igor Kovalchuk

    1. Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada

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  • 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 1456)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis

    • Wanhui You, Stéphane Pien, Ueli Grossniklaus
    Pages 1-13

  3. Chromatin Conformation Capture-Based Analysis of Nuclear Architecture

    • Stefan Grob, Ueli Grossniklaus
    Pages 15-32

  4. Meta-analysis of Genome-Wide Chromatin Data

    • Julia Engelhorn, Franziska Turck
    Pages 33-50

  5. Localization of miRNAs by In Situ Hybridization in Plants Using Conventional Oligonucleotide Probes

    • Sara Hernández-Castellano, Geovanny I. Nic-Can, Clelia De-la-Peña
    Pages 51-62

  6. The Combined Bisulfite Restriction Analysis (COBRA) Assay for the Analysis of Locus-Specific Changes in Methylation Patterns

    • Andriy Bilichak, Igor Kovalchuk
    Pages 63-71

  7. Analysis of Global Genome Methylation Using the Cytosine-Extension Assay

    • Andriy Bilichak, Igor Kovalchuk
    Pages 73-79

  8. In Situ Analysis of DNA Methylation in Plants

    • Palak Kathiria, Igor Kovalchuk
    Pages 81-88

  9. Analysis of DNA Hydroxymethylation Using Colorimetric Assay

    • Andrey Golubov, Igor Kovalchuk
    Pages 89-97

  10. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP)

    • María Ángeles Guevara, Nuria de María, Enrique Sáez-Laguna, María Dolores Vélez, María Teresa Cervera, José Antonio Cabezas
    Pages 99-112

  11. Differentially Methylated Region-Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify DMRs in Uncharacterized Genomes

    • Pavlina Sasheva, Ueli Grossniklaus
    Pages 113-125

  12. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays

    • Martine Boccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, David Baulcombe et al.
    Pages 127-139

  13. Northern Blotting Techniques for Small RNAs

    • Todd Blevins
    Pages 141-162

  14. Stem-Loop qRT-PCR for the Detection of Plant microRNAs

    • Erika Varkonyi-Gasic
    Pages 163-175

  15. Profiling New Small RNA Sequences

    • Masayuki Tsuzuki, Yuichiro Watanabe
    Pages 177-188

  16. Small RNA Library Preparation and Illumina Sequencing in Plants

    • Andriy Bilichak, Andrey Golubov, Igor Kovalchuk
    Pages 189-196

  17. Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow

    • Slava Ilnytskyy, Andriy Bilichak
    Pages 197-224

  18. Increasing a Stable Transformation Efficiency of Arabidopsis by Manipulating the Endogenous Gene Expression Using Virus-Induced Gene Silencing

    • Andriy Bilichak, Igor Kovalchuk
    Pages 225-236

  19. The Random Oligonucleotide-Primed Synthesis Assay for the Quantification of DNA Strand Breaks

    • Andriy Bilichak, Igor Kovalchuk
    Pages 237-242

  20. Profiling Transposable Elements and Their Epigenetic Effects in Non-model Species

    • Christian Parisod
    Pages 243-250
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Keywords

About this book

This volume provides a variety of protocols to analyze various epigenetic changes, including differential expression of non-coding RNAs, changes in DNA methylation, and histone modifications in plants. Chapters detail protocols with different degrees of complexity, and describe bioinformatics approaches for data processing and analysis. 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 Epigenetics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.


 

Editors and Affiliations

  • Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada

    Igor Kovalchuk

Bibliographic Information

  • Book Title: Plant Epigenetics

  • Book Subtitle: Methods and Protocols

  • Editors: Igor Kovalchuk

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4899-7708-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2017

  • Hardcover ISBN: 978-1-4899-7706-9Published: 22 October 2016

  • Softcover ISBN: 978-1-4939-7956-1Published: 07 July 2018

  • eBook ISBN: 978-1-4899-7708-3Published: 21 October 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 253

  • Number of Illustrations: 19 b/w illustrations, 32 illustrations in colour

  • Topics: Plant Sciences

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