DNA Methylation Protocols

ISBN-13: 9781493984992 / Angielski / Miękka / 2018 / 704 str.

Jorg Tost

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Introduction

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

Gitte Brinch Andersen and Jörg Tost

2. Considerations for Design and Analysis of DNA Methylation Studies

Karin B. Michels and Alexandra M. Binder

Part II Global DNA Methylation Levels

3. Quantification of Global DNA Methylation Levels by Mass Spectrometry

Agustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, and Mario F. Fraga

4. Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam Embryos

Nathalie 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® Ultralow Methyl-Seq Protocol

Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, and Jörg Tost

 

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

Dieter 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 Selection

William P. Accomando and Karin B. Michels

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

Julian R. Peat and Sébastien 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 Assays

John M. Greally

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

Xiaoyun 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. Clark

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16. A Guide to Illumina BeadChip Data Analysis

Michael C. Wu and Pei-Fen Kuan 

Part IV Highly Multiplexed Target Regions

17. Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite Sequencing

H. 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 Probes

Dinh Diep, Nongluk Plongthonkum, and Kun Zhang

20. Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System

Jennifer 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 Pul

verer, 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 Jörg Tost

23. Methylation-Specific PCR

João Ramalho-Carvalho, Rui Henrique, and Carmen Jerónimo

 

24. Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP)

Mary Jo Fackler and Saraswati Sukumar

25. MethyLight and Digital MethyLight

Mihaela Campan, Daniel J. Weisenberger, Bin Trinh, and Peter W. Laird

26. Quantitative Region-Specific DNA Methylation Analysis by the EPITY

PERTM Technology

Sonja Kunze

27. Methylation-Specific Multiplex Ligation-Dependent P

robe 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 Chromosomes

Pascal Giehr and Jörn Walter

30. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences

Susan 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 Analysis

Akram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg

32. DNA Methylation Analysis of Free-Circulating DNA in Body Fluids

Maria 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-Hydroxymethylcytosine

John P. Thomson and Richard R. Meehan

Blurb

This third edition volume expands on the previous editions with 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 reag

ents, 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.