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Updated: May 26, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
Published on: December 12, 2017
Measuring nucleosome occupancy in vivo by micrococcal nuclease
1Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. g-bryant@ski.mskcc.org
Abstract:
Eukaryotic genomes are wrapped in nucleosomes. These nucleosomes could be a barrier or could help facilitate the binding of transcription or replication factors. To understand what biological role nucleosomes play, an accurate and reliable method for measuring not only the position of a nucleosome but the fraction of the population that is bound by a nucleosome is needed. Here is described a method for determining nucleosome occupancy that takes advantage of the difference in the rate of digestion of DNA by micrococcal nuclease when naked DNA is compared to the same DNA bound by a nucleosome. Curve fitting to a function that describes the amount of DNA remaining following a series of digestions over a broad range of micrococcal nuclease allows the calculation of nucleosome occupancy anywhere in the genome under many different conditions in vivo.
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