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Chromatin Protocols

  • Book
  • © 2009

Overview

Editors:
  1. Srikumar P. Chellappan

    1. Research Institute, H. Lee Moffitt Cancer Center &, Tampa, U.S.A.

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  • Provides an easily accessible reference volume for analysis of chromatin structure and function incorporating the latest techniques
  • Includes detailed, step by step guidelines for the analysis of chromatin structure and its role in transcription, replication and other biological processes
  • Details elaborate protocols for the detection and characterization of histone modifications including acetylation, methylation and ubiquitination
  • Describes protocols for techniques ranging from immunohistochemical detection of chromatin modifications to genome-wide analysis of chromatin associated proteins
  • Acts as a comprehensive guide to the most up to date techniques dealing with all aspects of chromatin biology
  • Presents experimental details in an easy to follow modular format typical of the MiMB series
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 523)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Preparation of Chromatin Assembly Extracts from Preblastoderm Drosophila Embryos

    • Edgar Bonte, Peter B. Becker
    Pages 1-10

  3. Analysis of Reconstituted Chromatin Using a Solid-Phase Approach

    • Raphael Sandaltzopoulos, Peter B. Becker
    Pages 11-25

  4. In Vivo Chromatin Decondensation Assays: Molecular Genetic Analysis of Chromatin Unfolding Characteristics of Selected Proteins

    • Sherry L. Winter, Philip Wong, Mark G. Alexandrow
    Pages 27-40

  5. DNA Methyltransferase Probing of Chromatin Structure Within Populations and on Single Molecules

    • Carolina Pardo, Scott A. Hoose, Santhi Pondugula, Michael P. Kladde
    Pages 41-65

  6. Visualization of the Expression of HMGN Nucleosomal Binding Proteins in the Developing Mouse Embryo and in Adult Mouse Tissues

    • Takashi Furusawa, Michael Bustin
    Pages 67-82

  7. Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin

    • Eisuke Gotoh
    Pages 83-92

  8. Analysis of DNA Topology in Yeast Chromatin

    • Randall H. Morse
    Pages 93-108

  9. Preparation and Analysis of Uniquely Positioned Mononucleosomes

    • Daria A. Gaykalova, Olga I. Kulaeva, Vladimir A. Bondarenko, Vasily M. Studitsky
    Pages 109-123

  10. Monitoring DNA Breaks in Optically Highlighted Chromatin in Living Cells by Laser Scanning Confocal Microscopy

    • Michael J. Kruhlak, Arkady Celeste, André Nussenzweig
    Pages 125-140

  11. Methods to Study Transcription-Coupled Repair in Chromatin

    • Hélène Gaillard, Ralf Erik Wellinger, Andrés Aguilera
    Pages 141-159

  12. Cytometric Analysis of DNA Damage: Phosphorylation of Histone H2AX as a Marker of DNA Double-Strand Breaks (DSBs)

    • Toshiki Tanaka, Dorota Halicka, Frank Traganos, Zbigniew Darzynkiewicz
    Pages 161-168

  13. Detection of DNA Damage Induced by Topoisomerase II Inhibitors, Gamma Radiation and Crosslinking Agents Using the Comet Assay

    • Lori A. Hazlehurst
    Pages 169-176

  14. Analysis of Genomic Aberrations Using Comparative Genomic Hybridization of Metaphase Chromosomes

    • Melanie Carless
    Pages 177-202

  15. In Vitro Replication Assay with Mammalian Cell Extracts

    • Wasia Rizwani, Srikumar P. Chellappan
    Pages 203-216

  16. Investigation of Genomic Methylation Status Using Methylation-Specific and Bisulfite Sequencing Polymerase Chain Reaction

    • Melanie Carless
    Pages 217-234

  17. Biochemical Analysis of Arginine Methylation in Transcription

    • Marc Tini, Hina Naeem, Joseph Torchia
    Pages 235-247

  18. In Vitro Histone Demethylase Assays

    • Kenji Kokura, Jia Fang
    Pages 249-261

  19. Histone Chaperone as Coactivator of Chromatin Transcription: Role of Acetylation

    • Shrikanth S. Gadad, Jayasha Shandilya, Venkatesh Swaminathan, Tapas K. Kundu
    Pages 263-278

  20. Histone Deacetylase Activity Assay

    • Zhigang Yuan, Natalie Rezai-Zadeh, Xiaohong Zhang, Edward Seto
    Pages 279-293
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Keywords

About this book

Significant advancements have been made in the study of chromatin structure and function over the past fifty years but none as spectacular as those made in the last decade due to the development of novel techniques and the ability to sequence large stretches of DNA. In Chromatin Protocols, Second Edition, expert researchers delineate these cutting-edge techniques via step-by-step laboratory methods and protocols, which encompass a wide array of topics from the isolation of nucleosomes, assembly of nucleosomes and study of the basic chromatin structure to detailed analysis of histone modifications and chromatin function. Written in the highly successful Methods in Molecular Biology™ series style, chapters include brief introductions to the subjects, lists of the necessary materials and reagents, readily reproducible protocols, and Notes sections which highlight tips on troubleshooting and avoiding known pitfalls.

Comprehensive and up-to-date, Chromatin Protocols, Second Edition is a valuable tool for scientists studying various aspects of chromatin function and an ideal guide to aid in the development of new techniques as well as new ideas in the field of chromatin biology.

Reviews

From the reviews of the second edition: “This book contains a collection of detailed and useful procedures concerning chromatin analysis. It includes methods for the isolation and assembly of nucleosomes, the analysis of basic chromatin structure, the covalent modification of histones and the analysis of chromatin function. … In summary, this is a very useful text, with lots of strengths … .” (Ray Waters, Human Genetics, Vol. 126, 2009)

Editors and Affiliations

  • Research Institute, H. Lee Moffitt Cancer Center &, Tampa, U.S.A.

    Srikumar P. Chellappan

Bibliographic Information

  • Book Title: Chromatin Protocols

  • Editors: Srikumar P. Chellappan

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-190-1

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2009

  • Hardcover ISBN: 978-1-58829-873-7Published: 13 March 2009

  • Softcover ISBN: 978-1-4939-5626-5Published: 23 August 2016

  • eBook ISBN: 978-1-59745-190-1Published: 21 April 2009

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIII, 416

  • Topics: Biochemistry, general, Nucleic Acid Chemistry, Gene Expression

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