Methods of Epigenetic Analysis -- Chromatin Immunoprecipitation Assays -- Native Chromatin Immunoprecipitation -- Q-PCR in Combination With ChIP Assays to Detect Changes in Chromatin Acetylation -- Restriction Endonuclease Accessibility as a Determinant of Altered Chromatin Structure -- Measuring Changes in Chromatin Using Micrococcal Nuclease -- DNaseI Hypersensitivity Analysis of Chromatin Structure -- Inhibition of Histone Deacetylases -- Site-Specific Analysis of Histone Methylation and Acetylation -- Analysis of Mammalian Telomere Position Effect -- Activity Assays for Poly-ADP Ribose Polymerase -- Multigenerational Selection and Detection of Altered Histone Acetylation and Methylation Patterns -- Profiling DNA Methylation by Bisulfite Genomic Sequencing -- Methylation-Sensitive Single-Strand Conformation Analysis -- SIRPH Analysis -- Real-Time PCR-Based Assay for Quantitative Determination of Methylation Status -- Denaturing Gradient Gel Electrophoresis to Detect Methylation Changes in DNA -- Photocrosslinking Oligonucleotide Hybridization Assay for Concurrent Gene Dosage and CpG Methylation Analysis -- Methylation-Specific Oligonucleotide Microarray -- Methylation-Specific PCR In Situ Hybridization -- Relative Quantitation of DNA Methyltransferase mRNA by Real-Time RT-PCR Assay -- DMB (DNMT-Magnetic Beads) Assay.

Recent advances in epigenetic research as well as the development of exciting new technologies have helped greatly in unraveling the many mysteries of nontraditional genetic processes. In Epigenetics Protocols, hands-on researchers describe 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. The protocols follow the successful Methods in Molecular Biology™ series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Epigenetics Protocols offers investigators readily reproducible techniques that will further promote progress in this critically important field.