Main description:

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.

Contents:

Preface...Table of Contents...Contributing Authors...

Part I Introduction
1. A Summary of the Biological Processes, Disease-Associated Changes and Clinical Applications of DNA MethylationGitte Brinch Andersen and Joerg Tost
2. Considerations for Design and Analysis of DNA Methylation StudiesKarin B. Michels and Alexandra M. Binder
Part II Global DNA Methylation Levels
3. Quantification of Global DNA Methylation Levels by Mass SpectrometryAgustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesus Canal, and Mario F. Fraga
4. Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam EmbryosNathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, and Sari Pennings
Part III Genome-Wide DNA Methylation Analysis
5. Whole-Genome Bisulfite Sequencing Using the Ovation (R) Ultralow Methyl-Seq ProtocolChristian Daviaud, Victor Renault, Florence Mauger, Jean-Francois Deleuze, and Joerg Tost 6. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite SequencingDieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, and Christoph Plass
7. Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing
Fumihito Miura and Takashi Ito
8. Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size SelectionWilliam P. Accomando and Karin B. Michels
9. Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging ApproachJulian R. Peat and Sebastien A. Smallwood

10. Methyl-CpG Binding Domain Sequencing: MBD-seq
Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey Shabalin, and Edwin J.C.G. van den Oord

11. The HELP-Based AssaysJohn M. Greally
12. Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seqXiaoyun Xing, Bo Zhang, Daofeng Li, and Ting Wang
13. Digital Restriction Enzyme Analysis of Methylation (DREAM)Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu, and Jean-Pierre J. Issa
14. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)Fides D. Lay, Theresa K. Kelly, and Peter A. Jones
15. Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, and Susan J. Clarkdiv>
16. A Guide to Illumina BeadChip Data AnalysisMichael C. Wu and Pei-Fen Kuan
Part IV Highly Multiplexed Target Regions

17. Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite SequencingH. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, and Daniel R. Salomon
18. Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)Martyna Adamowicz-Brice, Klio Maratou, and Timothy J. Aitman
19. Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock ProbesDinh Diep, Nongluk Plongthonkum, and Kun Zhang
20. Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment SystemJennifer Wendt, Heidi Rosenbaum, Todd Richmond, Jeffrey A. Jeddeloh, and Daniel Burgess

21. Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes " MSRE-qPCR "Gabriel Beikirch, Walter Pulverer, Manuela Hofner, Christa Noehammer, and Andreas Weinhaeusel

Part V Locus-Specific DNA Methylation Analysis
22. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing
Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo G. Gut, and Joerg Tost
23. Methylation-Specific PCRJoao Ramalho-Carvalho, Rui Henrique, and Carmen Jeronimo 24. Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP)Mary Jo Fackler and Saraswati Sukumar
25. MethyLight and Digital MethyLightMihaela Campan, Daniel J. Weisenberger, Bin Trinh, and Peter W. Laird

26. Quantitative Region-Specific DNA Methylation Analysis by the EPITYPERTM TechnologySonja Kunze
27. Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) Cathy B. Moelans, Lilit Atanesyan, Suivi P. Savola, and Paul J. van Diest
28. Methylation - Sensitive - High Resolution Melting (MS-HRM)Dianna Hussmann and Lise Lotte Hansen

29. Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual ChromosomesPascal Giehr and Joern Walter
30. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA SequencesSusan M. Mitchell, Keith N. Rand, Zheng-Zhou Xu, Thu Ho, Glenn S. Brown, Jason P. Ross, and Peter L. Molloy

Part VI DNA Methylation Analysis of Specific Biological Samples
31. DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation AnalysisAkram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg
32. DNA Methylation Analysis of Free-Circulating DNA in Body FluidsMaria Jung, Glen Kristiansen, and Dimo Dietrich
Part VII Hydroxymethylation
33. Tet-Assisted Bisulfite Sequencing (TAB-seq)Miao Yu, Dali Han, Gary C, Won, and Chuan He
34. Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)Kristina Kirschner, Felix Krueger, Anthony R. Green, and Tamir Chandra
35. Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-HydroxymethylcytosineJohn P. Thomson and Richard R. Meehan