DNase-seq (DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions sensitive to cleavage by DNase I.
[1][2][3] FAIRE-Seq is a successor of DNase-seq for the genome-wide identification of accessible DNA regions in the genome.
Both the protocols for identifying open chromatin regions have biases depending on underlying nucleosome structure.
[4] DNase-seq requires some downstream bioinformatics analyses in order to provide genome-wide DNA footprints.
[7] Site-centric methods, on the other hand, find footprints given the open chromatin profile around motif-predicted binding sites, i.e., regulatory regions predicted using DNA-protein sequence information (encoded in structures such as Position weight matrix).