DNA Methylation 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

      PDF

   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

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.

• DNA
• cytosines
• gene expression
• chromatin remodeling
• molecular assays
• pyrosequencing
• single CpG positions
• methylation-specific PCR

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

  Jörg Tost

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