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DNA Methylation Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Jörg Tost

    1. Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie Francois Jacob, Evry, France

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    You can also search for this editor in PubMed   Google Scholar

  • 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 1708)

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Table of contents (35 protocols)

  1. Front Matter

    Pages i-xviii
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation

      • Gitte Brinch Andersen, Jörg Tost
      Pages 3-30

    3. Considerations for Design and Analysis of DNA Methylation Studies

      • Karin B. Michels, Alexandra M. Binder
      Pages 31-46

  3. Global DNA Methylation Levels

    1. Front Matter

      Pages 47-47
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    2. Quantification of Global DNA Methylation Levels by Mass Spectrometry

      • Agustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, Mario F. Fraga
      Pages 49-58

    3. Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos

      • Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings
      Pages 59-80

  4. Genome-Wide DNA Methylation Analysis

    1. Front Matter

      Pages 81-81
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    2. Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol

      • Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost
      Pages 83-104

    3. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing

      • Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils et al.
      Pages 105-122

    4. Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing

      • Fumihito Miura, Takashi Ito
      Pages 123-136

    5. Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection

      • William P. Accomando Jr., Karin B. Michels
      Pages 137-159

    6. Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach

      • Julian R. Peat, Sébastien A. Smallwood
      Pages 161-169

    7. Methyl-CpG-Binding Domain Sequencing: MBD-seq

      • Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey A. Shabalin, Edwin J. C. G. van den Oord
      Pages 171-189

    8. The HELP-Based DNA Methylation Assays

      • John M. Greally
      Pages 191-207

    9. Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq

      • Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang
      Pages 209-246

    10. Digital Restriction Enzyme Analysis of Methylation (DREAM)

      • Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu et al.
      Pages 247-265

    11. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)

      • Fides D. Lay, Theresa K. Kelly, Peter A. Jones
      Pages 267-284

    12. Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)

      • Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, Susan J. Clark
      Pages 285-302

    13. A Guide to Illumina BeadChip Data Analysis

      • Michael C. Wu, Pei-Fen Kuan
      Pages 303-330
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Keywords

About this book

This third edition volume expands on the previous editions by providing a comprehensive update on the available technologies required to successfully perform DNA methylation analysis. The different technologies discussed in this book analyze the global DNA methylation contents, comprehensive analyses using various NGS based methods for genome-wide DNA methylation analysis, along with precise quantification of DNA methylation levels on single CpG positions. The chapters in this book are divided into 7 parts: an introduction to the field along with tips on study design and data analysis; global DNA methylation levels; genome-wide DNA methylation analysis; highly multiplexed target regions; locus-specific DNA methylation analysis; DNA methylation analysis of specific biological samples; and hydroxymethylation. 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 thorough, DNA Methylation Protocols, Third Edition is a valuable resource for postdoctoral investigators and research scientists who work with different aspects of genetics, and cellular and molecular biology, as well as clinicians who are involved in diagnostics or treatment of diseases with epigenetic components.


Editors and Affiliations

  • Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie Francois Jacob, Evry, France

    Jörg Tost

Bibliographic Information

  • Book Title: DNA Methylation Protocols

  • Editors: Jörg Tost

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7481-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2018

  • Hardcover ISBN: 978-1-4939-7479-5Published: 10 December 2017

  • Softcover ISBN: 978-1-4939-8499-2Published: 30 August 2018

  • eBook ISBN: 978-1-4939-7481-8Published: 09 December 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: XVIII, 704

  • Number of Illustrations: 35 b/w illustrations, 67 illustrations in colour

  • Topics: Human Genetics

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