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The field of epigenetics has played a major role at the forefront not only of molecular biology, but also of medical genetics and clinical medicine. Few disciplines have experienced growth comparable to that which we have witnessed for epigenetics in the past decade. The goal of Epigenetics Protocols, Second Edition is to highlight select techniques that have been mainstays in the field as well as to cover methods that are especially relevant to extant discoveries in epigenetics. This volume focuses on the two broad areas of epigenetics: DNA methylation and chromatin modifications, and also covers the complex topic of computational methods for epigenetic analyses which is essential to a complete understanding of the vast body of information that is being derived with the use of these newly-developed tools. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Epigenetics Protocols, Second Edition serves as an ideal guide to advanced students, basic scientists and clinical researchers as well as clinicians and biotechnology investigators who wish to continue exploring this exciting and progressive research field.
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Table of Contents

1. Advances in Epigenetic Technology Trygve O. Tollefsbol 2. DNA Methylation Detection: Bisulfite Genomic Sequencing Analysis Yuanyuan Li and Trygve O. Tollefsbol 3. Methylation-specific PCR (MSP) Ja-Lok Ku, You-Kyung Jeon, and Jae-Gahb Park 4. Analyzing DNA Methylation Using Bisulfite Pyrosequencing Thomas Mikeska, Joerg Felsberg, Chelsee A. Hewitt, and Alexander Dobrovic 5. Closed-tube PCR Methods for Locus Specific DNA Methylation Analysis Ida L. M. Candiloro, Thomas Mikeska, and Alexander Dobrovic 6. A Combined Bisulfite Restriction Analysis (COBRA) Bioinformatics Tool: Methyl-typing Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang 7. SIRPH: an HPLC-based SNuPE for Quantitative Methylation Measurement at Specific CpG Sites Heike Singer, Nicole Nusgen, and Osman El-Maarri 8. Restriction Landmark Genome Scanning (RLGS) Hisato Okuizumi, Tomoko Takamiya, Yasushi Okazaki, and Yoshihide Hayashizaki 9. Methylated DNA Immunoprecipitation (MeDIP) Genome-wide Analysis Mattia Pelizzola and Annette Molinaro 10. Methylated-CpG Island Recovery Assay (MIRA) Natalie Mitchell, J. Tyson DeAngelis, and Trygve O. Tollefsbol 11. Global DNA Methylation Analysis Using the Luminometric Methylation Assay, LUMA Mohsen Karimi, Karin Luttropp, and Tomas J. Ekstroem 12. Inhibition of DNA Methylation in Somatic Cells Angelica M. Giraldo and Kenneth R. Bondioli 13. DNA Methyltransferase Assays Renata Z. Jurkowska, Alexandre Ceccaldi, Yingying Zhang, Paola B. Arimondo, and Albert Jeltsch 14. A Chromatin Immunoprecipitation Protocol for Small Cell Numbers Philippe Collas 15. Native Chromatin Immunoprecipitation (nChIP) Celine Cosseau and Christoph Grunau 16. Q-PCR in Combination with ChIP Assays to Detect Changes in Chromatin Acetylation Ryan A. Irvine, Cindy Okitsu, and Chih-Lin Hsieh 17. Sequential Chromatin Immunoprecipitation (SeqChIP) Assay and Analysis Ricardo B. de Medeiros 18. Combined Chromatin Immunoprecipitation and Bisulfite Methylation Sequencing (ChIP-BMS) Analysis Yuanyuan Li and Trygve O. Tollefsbol 19. Studying RNA-protein Interactions in vivo by RNA Immunoprecipitation (RIP) Luke A. Selth, Pierre Close, and Jesper Q. Svejstrup 20. Using ChIP-seq Technology to Generate High-resolution Profiles of HistoneModifications Henriette O'Geen, Lorigail Echipare, and Peggy J. Farnham 21. Mapping Open Chromatin with Formaldehyde-assisted Isolation of Regulatory Elements (FAIRE) Takao Nammo, Santiago A. Rodriguez-Segui, and Jorge Ferrer 22. Inhibition of Histone Deacetylases Yi Huang, Patrick G. Shaw, and Nancy E. Davidson 23. Computational Methods for Epigenetic Analysis - the Protocol of Computational Analysis for Modified Methylation-specific Digital Karyotyping (MMSDK) Based on Massively Parallel Sequencing Jian Li, Qian Zhao, and Lars Bolund

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