MNase titration reveals differences between nucleosome occupancy and chromatin accessibility View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-05-06

AUTHORS

Jakub Mieczkowski, April Cook, Sarah K. Bowman, Britta Mueller, Burak H. Alver, Sharmistha Kundu, Aimee M. Deaton, Jennifer A. Urban, Erica Larschan, Peter J. Park, Robert E. Kingston, Michael Y. Tolstorukov

ABSTRACT

Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. More... »

PAGES

11485

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms11485

    DOI

    http://dx.doi.org/10.1038/ncomms11485

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1025387004

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27151365


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