Success of any FAIRE-seq experiment heavily depends on adequate fixation efficiency that can alter depending on cell permeability, composition and a variety of other physiological factors. For most mammalian cells, 5 minutes of fixation time is usually ample [89]. Fungi and plants may require a much higher fixation time [15, 93] or improved fixation solutions [100] and optimization is necessary to avoid inconsistent results. Also, FAIRE has lower resolution in identifying open-chromatin at promoters of highly expressed genes compared to DNase-seq [94]. FAIRE’s major limitation, that far outweighs all benefits, is that it has a lower signal-to-noise ratio compared to the other chromatin accessibility assays. This high background makes computational data interpretation very difficult, with only strong recovered signal being informative.
