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Epigenetics Protocols

A collection of state-of-the-art methods for epigenetic analysis, including recent breakthrough techniques that have great potential in the rapidly expanding field of non-Mendelian genetics. The authors provide techniques for the analysis of chromatin remodeling, such as histone acetylation and methylation. In addition, methods in newly developed and especially promising areas of epigenetics, such as telomere position effects, quantitative epigenetics, and ADP ribosylation are covered. There is also an updated analysis of techniques involving DNA methylation and its role in the modification, as well as the maintenance, of chromatin structure. Of special interest are potentially revolutionary techniques. These include methods for determining changes in native chromatin, methods of microarray analysis applied to epigenetics, and methylation-sensitive single-strand conformation techniques. The methods are suitable not only for studying fundamental biological processes, but also for investigating possible therapeutic interventions and such diseases as cancer.
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Table of Contents

Methods of Epigenetic Analysis Trygve O. Tollefsbol Chromatin Immunoprecipitation Assays Yan Yan, Haobin Chen, and Max Costa Native Chromatin Immunoprecipitation Alan W. Thorne, Fiona A. Myers, and Tim R. Hebbes Q-PCR in Combination With ChIP Assays to Detect Changes in Chromatin Acetylation Ryan A. Irvine and Chih-Lin Hsieh Restriction Endonuclease Accessibility as a Determinant of Altered Chromatin Structure William M. Hempel and Pierre Ferrier Measuring Changes in Chromatin Using Micrococcal Nuclease Nicolas Steward and Hiroshi Sano DNaseI Hypersensitivity Analysis of Chromatin Structure Qianjin Lu and Bruce Richardson Inhibition of Histone Deacetylases Cheng Liu and Dawei Xu Site-Specific Analysis of Histone Methylation and Acetylation David Umlauf, Yuji Goto, and Robert Feil Analysis of Mammalian Telomere Position Effect Joseph A. Baur, Woodring E. Wright, and Jerry W. Shay Activity Assays for Poly-ADP Ribose Polymerase 1 Eva Kirsten, Ernest Kun, Jerome Mendeleyev, and Charles P. Ordahl Multigenerational Selection and Detection of Altered Histone Acetylation and Methylation Patterns: Toward a Quantitative Epigenetics in Drosophila Mark D. Garfinkel, Vincent E. Sollars, Xiangyi Lu, and Douglas M. Ruden Profiling DNA Methylation by Bisulfite Genomic Sequencing: Problems and Solutions Liang Liu, Rebecca C. Wylie, Nathaniel J. Hansen, Lucy G. Andrews, and Trygve O. Tollefsbol Methylation-Sensitive Single-Strand Conformation Analysis: A Rapid Method to Screen for and Analyze DNA Methylation Jean Benhattar and Genevieve Clement SIRPH Analysis: SNuPE With IP-RP-HPLC for Quantitative Measurements of DNA Methylation at Specific CpG Sites Osman El-Maarri Real-Time PCR-Based Assay for Quantitative Determination of MethylationStatus Ulrich Lehmann and Hans Kreipe Denaturing Gradient Gel Electrophoresis to Detect Methylation Changes in DNA Masahiko Shiraishi Photocrosslinking Oligonucleotide Hybridization Assay for Concurrent Gene Dosage and CpG Methylation Analysis Risa Peoples, Michael Wood, and Reuel Van Atta Methylation-Specific Oligonucleotide Microarray Pearlly S. Yan, Susan H. Wei, and Tim Hui-Ming Huang Methylation-Specific PCR In Situ Hybridization Gerard J. Nuovo Relative Quantitation of DNA Methyltransferase mRNA by Real-Time RT-PCR Assay John Attwood and Bruce Richardson DMB (DNMT-Magnetic Beads) Assay: Measuring DNA Methyltransferase Activity In Vitro Tomoki Yokochi and Keith D. Robertson Index


"Comprehensive and easy to use...offers investigators readily reproducible techniques that will further promote progress in this critically important field." - Tumori

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