Historically, open chromatin has been identified by the hypersensitivity of genomic sites to nuclease treatment with MNase and the non-specific double-strand endonuclease DNase I [61]. In a typical experiment, low concentrations of DNase I liberate accessible chromatin by preferentially cutting within nucleosome-free genomic regions characterized as DNase I hypersensitive sites (DHSs) (Figure 1). Early low-throughput experiments, provided the first demonstration that active genes have an altered chromatin conformation that makes them susceptible to digestion with DNase I [61]. Further research in Drosophila and other eukaryotes, supported the conserved observation that chromatin structure is disrupted during gene activation and that DHSs are the primary sites of active chromatin rendering access of trans-factors to regulatory elements [14, 27, 28, 62–65]. It has later been shown that DHSs result during gene activation [17], due to loss or temporal destabilization of one or more nucleosomes from cis-regulatory elements with the combinatorial action of ATP-dependent nucleosome- and histone-remodelers [20, 66, 67].
