One of the easiest methods for directly probing nucleosome-depleted areas of a genome is FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) (Figure 1), although the high background in the output data limits its usefulness [15, 86–89]. FAIRE is based on the phenol-chloroform separation of nucleosome-bound and free areas of a genome in the interphase and aqueous phase respectively. The procedure involves the initial crosslinking of chromatin with formaldehyde to capture in vivo protein-DNA interactions, and subsequent shearing of chromatin with sonication. Following phenol-chloroform extraction, nucleosome-depleted areas of the genome are released to the aqueous phase of the solution due to much higher crosslinking efficiency of histones to DNA, compared to other regulatory factors [87, 90]. The chromatin-accessible population of fragments can then be detected by quantitative PCR, tiling DNA microarrays [15, 86] or more recently with paired-end or single-end NGS (FAIRE-seq) [87, 91].
