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Analysis of Distant Communication on Defined Chromatin Templates In Vitro

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DNA-Protein Interactions

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 543))

Summary

Regulation of many biological processes in eukaryotes involves distant communication between the regulatory DNA sequences (e.g., enhancers) and their targets over the DNA regions organized in chromatin. However previously developed methods for analysis of communication in chromatin in vitro are artifact-prone and/or do not allow analysis of communication on physiologically relevant, saturated arrays of nucleosomes. Here we describe a method for quantitative analysis of the rate of distant communication in cis on saturated arrays of nucleosomes capable of forming the 30-nm chromatin fibers in vitro.

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Acknowledgments

This work was supported by NSF (0549593) and NIH (GM58650) grants to V.M.S. We would like to thank Dr. T. J. Richmond for providing the12Ă—177-601 plasmid containing an array of twelve 601 NPSs.

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  1. Department of Pharmacology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA

    Yury S. Polikanov & Vasily M. Studitsky

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  1. Yury S. Polikanov
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  2. Vasily M. Studitsky
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Correspondence to Vasily M. Studitsky .

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    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

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    Polikanov, Y.S., Studitsky, V.M. (2009). Analysis of Distant Communication on Defined Chromatin Templates In Vitro. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_33

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    • DOI: https://doi.org/10.1007/978-1-60327-015-1_33

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    • Print ISBN: 978-1-60327-014-4

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