Epigenetics Protocols

Epigenetics Protocols

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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 (TM) 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.
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Product details

  • Hardback | 304 pages
  • 154 x 234 x 24mm | 662.26g
  • Totowa, NJ, United States
  • English
  • 2004 ed.
  • XII, 304 p.
  • 158829336X
  • 9781588293367

Back cover copy

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(TM) 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.
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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
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Review quote

"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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