Epigenetics Protocols

1. Front Matter

   Pages i-xi

   PDF

2. Methods of Epigenetic Analysis

   • Trygve O. Tollefsbol

   Pages 1-8

3. Chromatin Immunoprecipitation Assays

   • Yan Yan, Haobin Chen, Max Costa

   Pages 9-19

4. Native Chromatin Immunoprecipitation

   • Alan W. Thorne, Fiona A. Myers, Tim R. Hebbes

   Pages 21-44

5. Q-PCR in Combination With ChIP Assays to Detect Changes in Chromatin Acetylation

   • Ryan A. Irvine, Chih-Lin Hsieh

   Pages 45-52

6. Restriction Endonuclease Accessibility as a Determinant of Altered Chromatin Structure

   • William M. Hempel, Pierre Ferrier

   Pages 53-63

7. Measuring Changes in Chromatin Using Micrococcal Nuclease

   • Nicolas Steward, Hiroshi Sano

   Pages 65-75

8. DNaseI Hypersensitivity Analysis of Chromatin Structure

   • Qianjin Lu, Bruce Richardson

   Pages 77-86

9. Inhibition of Histone Deacetylases

   • Cheng Liu, Dawei Xu

   Pages 87-97

10. Site-Specific Analysis of Histone Methylation and Acetylation

    • David Umlauf, Yuji Goto, Robert Feil

    Pages 99-120

11. Analysis of Mammalian Telomere Position Effect

    • Joseph A. Baur, Woodring E. Wright, Jerry W. Shay

    Pages 121-136

12. Activity Assays for Poly-ADP Ribose Polymerase

    • Eva Kirsten, Ernest Kun, Jerome Mendeleyev, Charles P. Ordahl

    Pages 137-149

13. Multigenerational Selection and Detection of Altered Histone Acetylation and Methylation Patterns

    • Mark D. Garfinkel, Vincent E. Sollars, Xiangyi Lu, Douglas M. Ruden

    Pages 151-168

14. Profiling DNA Methylation by Bisulfite Genomic Sequencing

    • Liang Liu, Rebecca C. Wylie, Nathaniel J. Hansen, Lucy G. Andrews, Trygve O. Tollefsbol

    Pages 169-179

15. Methylation-Sensitive Single-Strand Conformation Analysis

    • Jean Benhattar, Geneviève Clément

    Pages 181-193

16. SIRPH Analysis

    • Osman El-Maarri

    Pages 195-205

17. Real-Time PCR-Based Assay for Quantitative Determination of Methylation Status

    • Ulrich Lehmann, Hans Kreipe

    Pages 207-218

18. Denaturing Gradient Gel Electrophoresis to Detect Methylation Changes in DNA

    • Masahiko Shiraishi

    Pages 219-231

19. Photocrosslinking Oligonucleotide Hybridization Assay for Concurrent Gene Dosage and CpG Methylation Analysis

    • Risa Peoples, Michael Wood, Reuel Van Atta

    Pages 233-249

20. Methylation-Specific Oligonucleotide Microarray

    • Pearlly S. Yan, Susan H. Wei, Tim Hui-Ming Huang

    Pages 251-260

The field of epigenetics has grown exponentially in the past decade, and a steady flow of exciting discoveries in this area has served to move it to the forefront of molecular biology. Although epigenetics may previously have been considered a peripheral science, recent advances have shown considerable progress in unraveling the many mysteries of nontraditional genetic processes. Given the fast pace of epigenetic discoveries and the groundbreaking nature of these developments, a thorough treatment of the methods in the area seems timely and appropriate and is the goal of Epigenetics Protocols. The scope of epigenetics is vast, and an exhaustive analysis of all of the techniques employed by investigators would be unrealistic. However, this ™ volume of Methods in Molecular Biology covers three main areas that should be of greatest interest to epigenetics investigators: (1) techniques related to analysis of chromatin remodeling, such as histone acetylation and methylation; (2) methods in newly developed and especially promising areas of epigenetics such as telomere position effects, quantitative epigenetics, and ADP ribosylation; and (3) an updated analysis of techniques involving DNA methylation and its role in the modification, as well as the maintenance, of chromatin structure.

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

• Department of Biology, University of Alabama, Birmingham

  Trygve O. Tollefsbol

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