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Plant Epigenetics

Methods and Protocols

  • Book
  • © 2010

Overview

Editors:
  1. Igor Kovalchuk

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

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    You can also search for this editor in PubMed   Google Scholar

  2. Franz J. Zemp

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Invaluable research tool for all levels of investigators, from undergraduates to research scientists, who are interested in exploring one of the newest and most exciting aspects of molecular plant research
  • A comprehensive guide for studying the epigenetic phenomena in a variety of plant species
  • Detailed chapters that describe how to generate and analyze epigenetic data in plants
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 631)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Analysis of DNA Methylation in Plants by Bisulfite Sequencing

    • Andrea M. Foerster, Ortrun Mittelsten Scheid
    Pages 1-11

  3. Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE

    • Andrea M. Foerster, Jennifer Hetzl, Christoph Müllner, Ortrun Mittelsten Scheid
    Pages 13-22

  4. Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) Assay

    • Alex Boyko, Igor Kovalchuk
    Pages 23-31

  5. Detection of Changes in Global Genome Methylation Using the Cytosine-Extension Assay

    • Alex Boyko, Igor Kovalchuk
    Pages 33-39

  6. In Situ Analysis of DNA Methylation in Plants

    • Palak Kathiria, Igor Kovalchuk
    Pages 41-48

  7. Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length Polymorphism

    • Alex Boyko, Igor Kovalchuk
    Pages 49-62

  8. Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation Changes

    • Leonor Ruiz-García, Jose Antonio Cabezas, Nuria de María, María-Teresa Cervera
    Pages 63-74

  9. 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 75-86

  10. Northern Blotting Techniques for Small RNAs

    • Todd Blevins
    Pages 87-107

  11. qRT-PCR of Small RNAs

    • Erika Varkonyi-Gasic, Roger P. Hellens
    Pages 109-122

  12. Cloning New Small RNA Sequences

    • Yuko Tagami, Naoko Inaba, Yuichiro Watanabe
    Pages 123-138

  13. Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A: ChIP-chip Molecular Methods

    • Julia J. Reimer, Franziska Turck
    Pages 139-160

  14. Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis

    • Ulrike Göbel, Julia Reimer, Franziska Turck
    Pages 161-184

  15. Metaanalysis of ChIP-chip Data

    • Julia Engelhorn, Franziska Turck
    Pages 185-207

  16. Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein–DNA Binding Analyses in Arabidopsis

    • Stéphane Pien, Ueli Grossniklaus
    Pages 209-220

  17. cDNA Libraries for Virus-Induced Gene Silencing

    • Andrea T. Todd, Enwu Liu, Jonathan E. Page
    Pages 221-236

  18. Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) Assay

    • Alex Boyko, Igor Kovalchuk
    Pages 237-242

  19. Reporter Gene-Based Recombination Lines for Studies of Genome Stability

    • Palak Kathiria, Igor Kovalchuk
    Pages 243-252

  20. Plant Transgenesis

    • Alicja Ziemienowicz
    Pages 253-268
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Keywords

About this book

The discovery of DNA as the genetic material brought great hope to scientists all over the world. It was believed that many of the lingering questions in genetics and the mechanisms of heredity would fnally be answered. However, as often is the case in science, more qu- tions arose out of this discovery. What defnes a gene? What are the mechanisms of gene regulation? Further discovery and technological innovations brought about sequencing techniques that allowed the study of complete genomes from many organisms, including Arabidopsis and humans. Despite all the excitement surrounding these technologies, many features of the genome remained unclear. Peculiar characteristics in genome composition such as signifcant redundancy consisting of many repetitive elements and noncoding sequences, active transcriptional units with no protein product, and unusual sequences in promoter regions added to the mysteries of genetic make-up and gene regulation. Indeed, the more we discovered about the genome, the more diffcult it became to understand the complexity of cellular function and regulation. Out of the study of the intricacies of the genome and gene regulation, arose a new science that was independent of actual DNA changes, but critical in maintaining gene regulation and genetic stability. Epigenetics, literally translated as “above genetics,” is the science that describes the mechanisms of heritable changes in gene regulation that does not involve modifcations of DNA sequence. These changes may last through somatic cell division and, in some cases, throughout multiple generations.

Reviews

From the reviews:

“The book by Kovalchuk and Zemp is a successful attempt to provide the most recent approaches for identifying epigenetic variation in plants. … it is without doubts that the publication should be in every bookcase of molecular scientists interested in epigenetics. I can also recommend it for plant ecologists and evolutionists engaged in epigenetic variation in plants because some methods can be a good improvement of the currently commonly used approaches.” (Vit Latzel, Folia Geobotanica, Vol. 48, 2013)

Editors and Affiliations

  • Dept. Biological Sciences, University of Lethbridge, Lethbridge, Canada

    Igor Kovalchuk, Franz J. Zemp

Bibliographic Information

  • Book Title: Plant Epigenetics

  • Book Subtitle: Methods and Protocols

  • Editors: Igor Kovalchuk, Franz J. Zemp

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60761-646-7

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2010

  • Hardcover ISBN: 978-1-60761-645-0Published: 24 March 2010

  • Softcover ISBN: 978-1-4939-5756-9Published: 23 August 2016

  • eBook ISBN: 978-1-60761-646-7Published: 10 March 2010

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 273

  • Topics: Plant Genetics and Genomics, Biochemistry, general, Plant Sciences, Gene Expression

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