Functional annotation of accessible regions is factor-dependent and relies highly on the availability of accurate TF binding motifs and their relevant information content as well as the spatial and temporal interaction of TFs with DNA [84, 85]. Recent research supports that DNase I cleavage patterns are affected by the time of interaction of TF with their recognition sites, with depth of cleavage being proportional to residence time [85]. Consequently, transient TFs leave minimal or no detectable cut signatures and their binding cannot be identified with any of the current footprinting algorithms. In addition, cleavage signatures appear in genomic sites with no apparent protein binding, providing further support that footprint profiles may arise as a result of inherent DNase I cleavage bias instead of protein protection from enzymatic activity. Thus, to accurately characterize gene regulatory networks from accessibility data, we need comprehensive TF motif databases generated using in vivo/in vitro assays or computationally based de novo motif discovery algorithms. More importantly there is an imminent need to further investigate the applicability of DNase-seq, and ATAC-seq for that matter, to accurately detect
