Main description:

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.

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 Histone

Modifications

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