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Chromatin Immunoprecipitation to Verify or to Identify In Vivo Protein–DNA Interactions

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Plant Transcription Factors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 754))

Abstract

Chromatin immunoprecipitation (ChIP) is a valuable tool to detect the interaction in vivo between a DNA-associated protein and DNA fragments. Combined with approaches to assess gene expression in response to accumulation of a transcription factor, it is possible to identify direct responsive targets from targets that are indirectly responsive to accumulation of the transcription factor. ChIP may be used to confirm in vivo association of a transcriptional regulator with suspected target DNA fragments. ChIP may also be used to discover new targets, and when combined with high-throughput approaches to identify DNA fragments associated with a transcription factor, it may provide a tool to study the gene regulatory networks active during plant development and/or response to the environment. Furthermore, ChIP is also a powerful means to map epigenetic modifications within a genome.

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Acknowledgments

The authors would like to thank Jeanne Hartman for comments on the manuscript. This work was supported by grants from the National Science Foundation (IBN-9984274 and IOS-0922845).

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Authors and Affiliations

  1. Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA

    Yumei Zheng & Sharyn E. Perry

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  1. Yumei Zheng
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  2. Sharyn E. Perry
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Correspondence to Sharyn E. Perry .

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Editors and Affiliations

  1. College of Agriculture, Dept. Plant & Soil Sciences, University of Kentucky, University Drive 1401, Lexington, 40546-0236, Kentucky, USA

    Ling Yuan

  2. Dept. Plant & Soil Sciences, University of Kentucky, Veterans Dr. 1405, Lexington, 40546-0312, Kentucky, USA

    Sharyn E. Perry

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Zheng, Y., Perry, S.E. (2011). Chromatin Immunoprecipitation to Verify or to Identify In Vivo Protein–DNA Interactions. In: Yuan, L., Perry, S. (eds) Plant Transcription Factors. Methods in Molecular Biology, vol 754. Humana Press. https://doi.org/10.1007/978-1-61779-154-3_16

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  • DOI: https://doi.org/10.1007/978-1-61779-154-3_16

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-153-6

  • Online ISBN: 978-1-61779-154-3

  • eBook Packages: Springer Protocols

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