Skip to Content
Merck

Genome-scale mapping of DNase I hypersensitivity.

Current protocols in molecular biology (2013-07-04)
Sam John, Peter J Sabo, Theresa K Canfield, Kristen Lee, Shinny Vong, Molly Weaver, Hao Wang, Jeff Vierstra, Alex P Reynolds, Robert E Thurman, John A Stamatoyannopoulos
ABSTRACT

DNase I-seq is a global and high-resolution method that uses the nonspecific endonuclease DNase I to map chromatin accessibility. These accessible regions, designated as DNase I hypersensitive sites (DHSs), define the regulatory features, (e.g., promoters, enhancers, insulators, and locus control regions) of complex genomes. In this unit, methods are described for nuclei isolation, digestion of nuclei with limiting concentrations of DNase I, and the biochemical fractionation of DNase I hypersensitive sites in preparation for high-throughput sequencing. DNase I-seq is an unbiased and robust method that is not predicated on an a priori understanding of regulatory patterns or chromatin features.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Sucrose, BioUltra, for molecular biology, ≥99.5% (HPLC)
Sigma-Aldrich
Proteinase K from Tritirachium album, buffered aqueous glycerol solution, for molecular biology, ≥800 units/mL
Sigma-Aldrich
1,4-Dithioerythritol, BioXtra, ≥99.0%
Sigma-Aldrich
IGEPAL® CA-630, for molecular biology