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Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo

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Chromatin Protocols

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

Abstract

Studies in the past decade have shown that differential gene expression depends not only on the binding of specific transcription factors to discrete promoter elements but also on the epigenetic modification of the DNA as well as histones associated with the promoter. While techniques like electrophoretic mobility shift assays could detect and characterize the binding of specific transcription factors present in cell lysates to DNA sequences in in vitro binding conditions, they were not effective in assessing the binding in intact cells. Development of chromatin immunoprecipitation technique in the past decade enabled the analysis of the association of regulatory molecules with specific promoters or changes in histone modifications in vivo, without overexpressing any component. ChIP assays can provide a snapshot of how a regulatory transcription factor affects the expression of a single gene or a variety of genes at the same time. Availability of high-quality antibodies that recognizes histones modified in a specific fashion further expanded the use of ChIP assays to analyze even minute changes in histone modification and nucleosomes structure. This chapter outlines the general strategies and protocols used to carry out ChIP assays to study the differential recruitment of transcription factors as well as histone modifications.

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Acknowledgments

Work in the Chellappan lab is supported by the grants CA63136, CA77301 and CA127725 from the NCI.

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Authors and Affiliations

  1. Drug Discovery Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA

    Smitha Pillai, Piyali Dasgupta & Srikumar P. Chellappan

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  1. Smitha Pillai
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  2. Piyali Dasgupta
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  3. Srikumar P. Chellappan
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Editors and Affiliations

  1. Research Institute, H. Lee Moffitt Cancer Center &, Magnolia Drive 12902, Tampa, 33612, U.S.A.

    Srikumar P. Chellappan

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Pillai, S., Dasgupta, P., Chellappan, S.P. (2009). Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo. In: Chellappan, S. (eds) Chromatin Protocols. Methods in Molecular Biology, vol 523. Humana Press. https://doi.org/10.1007/978-1-59745-190-1_22

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  • DOI: https://doi.org/10.1007/978-1-59745-190-1_22

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-873-7

  • Online ISBN: 978-1-59745-190-1

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