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Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM #MMPMID25271716
Rodriguez J; McKnight JN; Tsukiyama T
Curr Protoc Mol Biol 2014[]; 108 (ä): 21.28.1-21.28.16 PMID25271716show ga
Because histones bind DNA very tightly, the location and occupancy of 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 advancement made such analyses feasible in a genome-wide scale at a high resolution. In addition, we have recently developed a method to measure nuclease accessibility of nucleosomes in a global scale. Here we describe methods to map nucleosome positions, to determine nucleosome density, and to determine nuclease accessibility of nucleosomes using deep sequencing.