Initially demonstrated to identify accessible regulatory elements in Saccharomyces cerevisiae[90], FAIRE has been extended to a wide range of eukaryotic cells and tissues, consistently demonstrating a negative relationship with nucleosome occupancy and an overlap with various cell type-specific marks of active chromatin [15, 45, 86, 87, 92, 93]. This assay has been instrumental for the identification of active regulatory elements in a number of human cell lines by ENCODE [26]. It has been used widely to detect open chromatin in normal and diseased cells [86, 91, 94, 95], to associate specific chromatin states with known sequence variants of disease susceptibility [91] or allele-specific signatures [96], and to decipher the effects of TF binding to chromatin structure [97, 98].
