DNA Methylation: Methods and Protocols

Part I: Introduction 1. DNA Methylation: An Introduction to the Biology and the Disease-Associated Changes of a Promising Biomarker Jörg Tost Part II: Global Methylation Levels 2. Quantification of Global DNA Methylation by Capillary Electrophoresis and Mass Spectrometry María Berdasco, Mario F. Fraga, and Manel Esteller 3. Methyl Group Acceptance Assay for the Determination of Global DNA Methylation Levels Kenneth P. Nephew, Curt Balch, and David G. Skalnik Part III: Methods for Whole Genome Analysis of DNA Methylation Patterns 4. Immunodetection Array Johannes Pröll, Christian Wechselberger, Mathilde Födermayr, Otto Zach, and Dieter Lutz 5. Methylated DNA Immunoprecipitation (MeDIP) Fabio Mohn, Dirk Schübeler, and Tim-Christoph Roloff 6. The MIRA Method for DNA Methylation Analysis Tibor A. Rauch and Gerd P. Pfeifer 7. The HELP Assay Mayumi Oda and John M. Greally 8. Differential Methylation Hybridization: Profiling DNA Methylation with a High Density CpG Island Microarray Pearlly S. Yan, Dustin Potter, Daniel E Deatherage, Shili Lin, and Tim H.-M. Huang 9. Analysis of DNA Methylation by Amplification of InterMethylated Sites (AIMS) Mireira Jordà, Jairo Rodriguez, Jordi Frigola, and Miguel A. Peinado 10. Methylation-Sensitive Representational Difference Analysis (MS-RDA) Toshikazu Ushijima and Satoshi Yamashita 11. Restriction Landmark Genomic Scanning: Analysis of CpG Islands in Genomes by 2D Gel Electrophoresis Joseph F. Costello, Dominic J. Smiraglia, Chibo Hong, and Christoph Plass 12. GoldenGate® Assay for DNA Methylation Profiling Marina Bibikova andJian-Bing Fan 13. 5'-Azacytidine Expression Arrays Paul Cairns Part IV: Gene Specific Methylation Analysis 14. DNA Methylation Analysis by Bisulfite Conversion, Cloning, and Sequencing of Individual Clones Yingying Zhang, Christian Rohde, Sascha Tierling, Heinrich Stamerjohanns, Richard Reinhardt, Jörn Walter, and Albert Jeltsch 15. Identification and Quantification of Differentially Methylated Loci by the PyrosequencingTM Technology Emelyne Dejeux , Hafida El abdalaoui, Ivo Glynne Gut, and Jörg Tost 16. Mass Spectrometric Analysis of Cytosine Methylation by Base-Specific Cleavage and Primer Extension Methods Dirk van den Boom and Mathias Ehrich 17. Melting Curve Assays for DNA Methylation Analysis Tomasz K. Wojdacz and Alexander Dobrovic 18. Methylation SNaPshot: A Method for Quantification of Site Specific DNA Methylation Levels Zachary Kaminsky and Arturas Petronis 19. Bio-COBRA: Absolute Quantification of DNA Methylation in Electrofluidics Chips Romulo Martin Brena and Christoph Plass 20. Restriction Digestion and Real-time PCR (qAMP) Christopher C. Oakes, Sophie La Salle, Jacquetta M. Trasler, and Bernard Robaire 21. MethylQuant : A Real-Time PCR Based Method to Quantify DNA Methylation at Single Specific Cytosines Claire Dugast-Darzacq and Thierry Grange 22. Methylation-Specific PCR Julien D. F. Licchesi and James G. Herman 23. MethyLight Mihaela Campan, Daniel J. Weisenberger, Binh Trinh, and Peter W. Laird 24. Quantification of Methylated DNA by HeavyMethyl Duplex PCR Jürgen Distler Part V: Special Applications 25. Analysis of Methylated Circulating