Historically, the simplest method to robustly identify active gene regulatory 
elements has been enzymatic digestion of nuclear DNA by nucleases such as 
DNaseI. Regions of extreme chromatin accessibility to DNaseI, commonly known as 
DNaseI hypersensitive sites, have been repeatedly shown to be markers for all 
types of active cis-acting regulatory elements, including promoters, enhancers, 
silencers, insulators, and locus control regions. However, the original 
classical method, which for over 25 years relied on Southern blot, was limited 
to studying only small regions of the genome. Here we describe the detailed 
protocol for DNase-chip, a high-throughput method that allows for a targeted or 
genome-wide identification of cis-acting gene regulatory elements.