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Methods Mol Biol. 2012;833:421-32. doi: 10.1007/978-1-61779-477-3_25.

Salt fractionation of nucleosomes for genome-wide profiling.

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Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.


Salt fractionation of nucleosomes, a classical method for defining "active" chromatin based on nucleosome solubility, has recently been adapted for genome-scale profiling. This method has several advantages for profiling chromatin dynamics, including general applicability to cell lines and tissues, quantitative recovery of chromatin, base-pair resolution of nucleosomes, and overall simplicity both in concept and execution. This chapter provides detailed protocols for nuclear isolation, chromatin fragmentation by micrococcal nuclease digestion, successive solubilization of chromatin fractions by addition of increasing concentrations of salt, and genome-wide analyses through microarray hybridization and next-generation sequencing.

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