title: Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM.
abstract: Because histones bind DNA very tightly, the location on DNA and the level of occupancy of a given DNA sequence by nucleosomes can profoundly affect accessibility of non-histone proteins to chromatin, affecting virtually all DNA-dependent processes, such as transcription, DNA repair, DNA replication and recombination. Therefore, it is often necessary to determine positions and occupancy of nucleosomes to understand how DNA-dependent processes are regulated. Recent technological advances made such analyses feasible on a genome-wide scale at high resolution. In addition, we have recently developed a method to measure nuclease accessibility of nucleosomes on a global scale. This unit describes methods to map nucleosome positions, to determine nucleosome density, and to determine nuclease accessibility of nucleosomes using deep sequencing.
authors.affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|These authors contributed equally to this work.
authors.forename: Jairo
authors.initials: J
authors.lastname: Rodriguez
authors.affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|These authors contributed equally to this work.
authors.forename: Jeffrey N
authors.initials: JN
authors.lastname: McKnight
authors.affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Toshio
authors.initials: T
authors.lastname: Tsukiyama
mesh_terms: D004261:DNA Replication / Q000502:physiology; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016681:Genome, Fungal / Q000502:physiology*; D055106:Genome-Wide Association Study / Q000379:methods*; D006657:Histones / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D006657:Histones; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins
keywords: chromatin accessibility; deep sequencing; genome-wide analysis; nucleosome occupancy; nucleosome positioning