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Contents Preface Contributors 1 Methods of Epigenetic Analysis Trygve O. Tollefsbol 2 Chromatin Immunoprecipitation Assays Yan Yan and Max Costa 3 Native Chromatin Immunoprecipitation Alan W. Thorne, Fiona Myers, and Tim R. Hebbes 4 Q-PCR in Combination with ChIP Assays to Detect Changes in Chromatin Acetylation Ryan A. Irvine and Chih-Lin Hsieh 5 Restriction Endonuclease Accessibility as a Determinant of Altered Chromatin Structure William M. Hempel and Pierre Ferrier 6 Measuring Changes in Chromatin Using Micrococcal Nuclease Nicolas Steward and Hiroshi Sano 7 DNaseI Hypersensitivity Analysis of Chromatin Structure Qianjin Lu and Bruce Richardson 8 Inhibition of Histone Deacetylases Cheng Liu and Dawei Xu 9 Site-Specific Analysis of Histone Methylation and Acetylation David UmLauf, Yuji Goto, and Robert Feil 10 Analysis of Mammalian Telomere Position Effect Joseph A. Baur, Woodring E. Wright, and Jerry W. Shay 11 Activity Assays for Poly-ADP Ribose Polymerase I Eva Kirsten, Ernest Kun, Jerome Mendeleyev, and Charles P. Ordahl 12 Multi-Generational Selection and Detection of Altered Histone Acetylation and Methylation Patters: Toward a "Quantitative Epigenetics" in Drosophila Mark D. Garfinkel, Vincent E. Sollars, Xiangyi Lu, and Douglas M. Ruden 13 Profiling DNA Methylation by Bisulfite Genomic Sequencing: Problems And Solutions Liang Liu, Rebecca Wylie, Nathan Hansen, Lucy Andrews, and Trygve O. Tollefsbol 14 Methylation-Sensitive Single-Stand Conformation Analysis: A Rapid Method to Screen for and Analyze DNA Methylation Jean Benhattar and Genevieva Clement 15 SIRPH Analysis: A Combined SNuPE with IP-RP-HPLC for Quantitative Methylation Measurements at Specific CpG Sites Osman El-Maarri 16 Real-Time PCR-Based Assay for Quantitative Determination of Methylation Status Ulrich Lehmann and Hans Kreipe 17 Denaturing Gradient Gel Electrophoresis to Detect Methylation Changes in DNA Mashiko Shiraishi 18 Photo-Cross-Linking Oligonucleotide Hybridization Assay for Concurrent Gene Dosage and CpG Methylation Analysis Risa Peoples, Michael Wood, and Reuel Van Atta 19 Methylation-Specific Oligonucleotide Microarray Pearlly S. Yan, Susan H. Wei, and Tim Hui-Ming Huang 20 Methylation-Specific PCR In Situ Hybridization Gerard J. Nuovo 21 Relative Quantitation of DNA Cethyltransferase mRNA by Real-Time RT-PCR Assay John Attwood and Bruce Richardson 22 DMB (DNMT-magnetic beads) Assay: Measuring DNA Methyltransferase Activity In Vitro Tomoki Yokochi and Keith D. Robertson Index
Library of Congress Subject Headings for this publication: Chromatin Laboratory manuals, Telomere Laboratory manuals, ADP-ribosylation Laboratory manuals, Epigenesis Laboratory manuals, Chromatin Assembly and Disassembly genetics Laboratory Manuals, Chromosome Structures metabolism Laboratory Manuals, DNA Methylation Laboratory Manuals, Epigenesis, Genetic Laboratory Manuals, Histone Code genetics Laboratory Manuals, Histones metabolism Laboratory Manuals