Protocols

• Nucleosome mobilization assay (Epigenome NoE)
  The organization of eukaryotic genomes into nucleosome arrays restricts DNA sequence accessibility to many nuclear factors. Thus most DNA-based processes require opening (or "re-closing") of these arrays. One major class of enzymes, the "chromatin/nucleosome remodeling" factors, uses ATP hydrolysis to alter the canonical histone-DNA contacts. The term "nucleosome remodeling" can be defined and monitored in different ways (Flaus and Owen-Hughes, 2004). The simplest configuration to study one aspect of nucleosome remodeling is to use a purely reconstituted system consisting of mononucleosomes and an ATP-dependent nucleosome remodeler in the so-called "nucleosome sliding" or "nucleosome mobilization" assay. This technique was initially developed by Carl Wu and Peter Becker laboratories (Hamiche et al., 1999; Langst et al., 1999) by taking advantage of two nucleosome properties: Nucleosomal histones can moderately move on DNA under rather mild temperature and salt conditions (Beard, 1978; Meersseman et al., 1991; Pennings et al., 1991) and nucleosomes reconstituted on a short DNA fragment can adopt multiple positions that can be separated by native gel electrophoresis (Linxweiler and Horz, 1984; Pennings et al., 1991).
  http://www.epigenome-noe.net/researchtools/protoco...
  Added: Mon Aug 04 2008, Hits: 40, Reviews: 0  Write review  
• Site-Directed Hydroxy Radical Mapping of Nucleosome Positions in vitro (Epigenome NoE)
  This protocol gives details of a method for mapping the position of nucleosomes in vitro by attaching an EDTA-derived reagent to a specific site on the histone octamer which then catalyses local DNA cleavage. The sites of cleavage reveal the position of the nucleosome at base pair resolution (Flaus et al., 1996; Flaus and Richmond, 1999a; Flaus and Richmond, 1999b; Bruno et al., 2004). Nucleosome positions and movements on DNA fragments of some 500 bp have been mapped
  http://www.epigenome-noe.net/researchtools/protoco...
  Added: Mon Aug 04 2008, Hits: 31, Reviews: 0  Write review