Genome‐Scale Mapping of DNase I Hypersensitivity

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