Overall, FAIRE enriches directly for areas of active chromatin, with the added benefit that the nucleosome-depleted regions are not degraded, it can be applied to any type of cells or tissue and that there is no requirement for initial preparation of cells and laborious enzyme titrations [15, 86, 89, 94]. FAIRE has been shown to identify additional distal regulatory elements not recovered by DNase-seq, although it remains unclear what these sites represent [94]. In addition, FAIRE overcomes the sequence-specific cleavage bias observed with MNase and DNase I, and thus represents an ancillary approach for these assays [52–54, 60, 99].
