Abstract
The nucleosome-scanning assay (NuSA) couples isolation of mononucleosomal DNA after micrococcal nuclease (MNase) digestion with quantitative real-time PCR (qPCR) to map nucleosome positions in chromatin. It is a relatively simple, rapid procedure that can produce a high-resolution map of nucleosome location and occupancy and thus is suitable for analyzing individual promoters in great detail. The analysis can also quantify the protection of DNA sequences due to interaction with proteins other than nucleosomes and show how this protection varies when conditions change. When coupled with chromatin immunoprecipitation (ChIP), NuSA can identify histone variants and modifications associated with specific nucleosomes.
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Acknowledgements
Research was supported by a grant from the General Medical Sciences Institute of the National Institutes of Health, GM26079 to E.T.Y. J.J. Infante was the recipient of a postdoctoral fellowship from the Ministry of Science and Innovation of Spain.
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Infante, J.J., Law, G.L., Young, E.T. (2012). Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. In: Morse, R. (eds) Chromatin Remodeling. Methods in Molecular Biology, vol 833. Humana Press. https://doi.org/10.1007/978-1-61779-477-3_5
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DOI: https://doi.org/10.1007/978-1-61779-477-3_5
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