Open AccessGenome‐Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High‐Resolution Histone ChIP, and NCAM
Author(s) -
Rodriguez Jairo,
McKnight Jeffrey N.,
Tsukiyama Toshio
Publication year - 2014
Publication title -
current protocols in molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.533
H-Index - 42
eISSN - 1934-3647
pISSN - 1934-3639
DOI - 10.1002/0471142727.mb2128s108
Subject(s) - nucleosome , histone , chromatin , micrococcal nuclease , chromatosome , linker dna , genetics , dna , computational biology , biology , microbiology and biotechnology
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. Curr. Protoc. Mol. Biol . 108:21.28.1‐21.28.16. © 2014 by John Wiley & Sons, Inc.