Figure 3

RED-seq captures the enhanced accessibility of open chromatin regions. Average RE accessibility (A, C) and nucleosome occupancy (B, D) [GEO:GSM1400766] of indicated chromatin domains. RED-seq or MNase-seq data are aligned on the centers of all peaks of DHSs (A-B), or CTCF binding sites (C-D), and averaged within a 2 kb region (-1000 to +1000 bp from the peaks). Normalized RE accessibility and RS density are shown. RE accessibility was normalized as in Figure 2. There are 159,331 DHSs [GEO:GSM1014154] (A-B), and 15,657 CTCF binding sites [GEO:GSE11431] (C-D) plotted. (E-F) Chromatin accessibility determined by RED-seq or DNase-seq and nucleosome occupancy are shown surrounding CTCF binding sites (E) or DHSs (F). Arrows indicate the phased peaks of RE accessibility found within linker regions.