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Plant Epigenetics and Epigenomics

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Charles Spillane

    1. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

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  2. Peter C. McKeown

    1. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

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  • Presents current up-to-date methodologies
  • Features tips on trouble shooting and avoiding known pitfalls
  • 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 1112)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Landscaping Plant Epigenetics

    • Peter C. McKeown, Charles Spillane
    Pages 1-24

  3. The Gene Balance Hypothesis: Dosage Effects in Plants

    • James A. Birchler, Reiner A. Veitia
    Pages 25-32

  4. High-Throughput RNA-Seq for Allelic or Locus-Specific Expression Analysis in Arabidopsis-Related Species, Hybrids, and Allotetraploids

    • Danny W-K. Ng, Xiaoli Shi, Gyoungju Nah, Z. Jeffrey Chen
    Pages 33-48

  5. Inference of Allele-Specific Expression from RNA-seq Data

    • Paul K. Korir, Cathal Seoighe
    Pages 49-69

  6. Screening for Imprinted Genes Using High-Resolution Melting Analysis of PCR Amplicons

    • Robert Day, Richard Macknight
    Pages 71-83

  7. Analysis of Genomic Imprinting by Quantitative Allele-Specific Expression by Pyrosequencing®

    • Peter C. McKeown, Antoine Fort, Charles Spillane
    Pages 85-104

  8. Endosperm-Specific Chromatin Profiling by Fluorescence-Activated Nuclei Sorting and Chip-on-Chip

    • Isabelle Weinhofer, Claudia Köhler
    Pages 105-115

  9. Imaging Sexual Reproduction in Arabidopsis Using Fluorescent Markers

    • Mathieu Ingouff
    Pages 117-124

  10. Genome-Wide Analysis of DNA Methylation in Arabidopsis Using MeDIP-Chip

    • Sandra Cortijo, René Wardenaar, Maria Colomé-Tatché, Frank Johannes, Vincent Colot
    Pages 125-149

  11. Methylation-Sensitive Amplified Polymorphism (MSAP) Marker to Investigate Drought-Stress Response in Montepulciano and Sangiovese Grape Cultivars

    • Emidio Albertini, Gianpiero Marconi
    Pages 151-164

  12. Detecting Histone Modifications in Plants

    • Jie Song, Bas Rutjens, Caroline Dean
    Pages 165-175

  13. Quantitatively Profiling Genome-Wide Patterns of Histone Modifications in Arabidopsis thaliana Using ChIP-seq

    • Chongyuan Luo, Eric Lam
    Pages 177-193

  14. Analysis of Retrotransposon Activity in Plants

    • Christopher DeFraia, R. Keith Slotkin
    Pages 195-210

  15. Detecting Epigenetic Effects of Transposable Elements in Plants

    • Christian Parisod, Armel Salmon, Malika Ainouche, Marie-Angèle Grandbastien
    Pages 211-217

  16. Detection and Investigation of Transitive Gene Silencing in Plants

    • Leen Vermeersch, Nancy De Winne, Ann Depicker
    Pages 219-241

  17. Back Matter

    Pages 243-245
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Keywords

About this book

Many fundamental discoveries concerning epigenetics and the elucidation of mechanisms of epigenetic regulation have developed from studies performed in plants. In Plant Epigenetics and Epigenomics: Methods and Protocols, leading scientists in the epigenetics field describe comprehensive techniques that have been developed to understand the plant epigenetic landscape. These include recently developed methods and techniques for analysis of epigenetically regulated traits, such as flowering time, transposon activation, genomic imprinting and genome dosage effects. 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 key tips on troubleshooting and avoidance of known pitfalls.

Authoritative and practical, Plant Epigenetics and Epigenomics: Methods and Protocols seek to aid scientists in the further study of plant epigenetic phenomena using advanced contemporary methods.

Editors and Affiliations

  • Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

    Charles Spillane, Peter C. McKeown

Bibliographic Information

  • Book Title: Plant Epigenetics and Epigenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Charles Spillane, Peter C. McKeown

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-773-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, New York 2014

  • Hardcover ISBN: 978-1-62703-772-3Published: 31 January 2014

  • Softcover ISBN: 978-1-4939-6229-7Published: 27 August 2016

  • eBook ISBN: 978-1-62703-773-0Published: 30 January 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 245

  • Number of Illustrations: 27 b/w illustrations, 12 illustrations in colour

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

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