title: Analysis of nucleosome positioning using a nucleosome-scanning assay.
abstract: The nucleosome-scanning assay (NuSA) couples isolation of mononucleosomal DNA after micrococcal nuclease (MNase) digestion with quantitative real-time PCR (qPCR) to map nucleosome positions in chromatin. It is a relatively simple, rapid procedure that can produce a high-resolution map of nucleosome location and occupancy and thus is suitable for analyzing individual promoters in great detail. The analysis can also quantify the protection of DNA sequences due to interaction with proteins other than nucleosomes and show how this protection varies when conditions change. When coupled with chromatin immunoprecipitation (ChIP), NuSA can identify histone variants and modifications associated with specific nucleosomes.
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Juan Jose
authors.initials: JJ
authors.lastname: Infante
authors.forename: G Lynn
authors.initials: GL
authors.lastname: Law
authors.forename: Elton T
authors.initials: ET
authors.lastname: Young
mesh_terms: D001681:Biological Assay / Q000379:methods*; D047369:Chromatin Immunoprecipitation; D004271:DNA, Fungal / Q000302:isolation & purification; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D059748:Proteolysis; D060888:Real-Time Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D013104:Spheroplasts / Q000166:cytology / Q000378:metabolism; D013223:Statistics as Topic
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D008836:Micrococcal Nuclease