For each cell line, four 15 cm culture dishes of approximately 90% confluent cells were cross-linked in 1% formaldehyde for 10 min at room temperature before lysing cells in SDS buffer and sonicating to shear genomic DNA to approximately 100-500 bp fragments. Insoluble cell debris was discarded, and the supernatant from pairs of dishes were combined to represent two biological replicates per cell line. The material was divided into aliquots for input, FAIRE and ChIP. Immunoprecipitations were performed overnight at 4°C using antibodies against H3K27ac (Abcam ab4729) and H3K4me1 (Abcam ab8895) followed by incubation with protein A/G agarose beads (Pierce). Following washing and elution from beads, the DNA was ethanol precipitated, and the pellet washed with 70% ethanol. Recovered DNA was re-suspended in water for sequencing. Purification and recovery of FAIRE material was performed as previously described in parallel with ChIP to ensure that annotation of open chromatin/nucleosome depletion was performed from the same cell lysate sample as annotation of histone acetylation and methylation marks.