title: MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.
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.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Jakub
authors.initials: J
authors.lastname: Mieczkowski
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: April
authors.initials: A
authors.lastname: Cook
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Bowman
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Britta
authors.initials: B
authors.lastname: Mueller
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Burak H
authors.initials: BH
authors.lastname: Alver
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Sharmistha
authors.initials: S
authors.lastname: Kundu
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Aimee M
authors.initials: AM
authors.lastname: Deaton
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Urban
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Erica
authors.initials: E
authors.lastname: Larschan
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Peter J
authors.identifier: 0000-0001-9378-960X
authors.initials: PJ
authors.lastname: Park
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D004331:Drosophila melanogaster; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D051379:Mice; D008836:Micrococcal Nuclease; D000066450:Mouse Embryonic Stem Cells; D058953:Neural Stem Cells; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D017423:Sequence Analysis, RNA
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D008836:Micrococcal Nuclease