Chromatin accessibility can be examined by DNase I digestion, and then revealed by the DNase I cleavage pattern. DNase I hypersensitive sites (DHSs) define the regulatory features of complex genomes (e.g., promoters, enhancers, insulators and other control regions).The combination of DNase I digestion and high-throughput sequencing (DNase-seq) has been used to map chromatin accessibility in vivo on a genome-wide scale. In this paper, we used this strategy to catalogue the CIS-regulatory elements of the developing mouse retina and brain.