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Epigenetics Protocols
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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 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

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