Figure 3

NF-κB binding in TNFα-regulated nucleosomal domains. ( A) A minority of p65 peaks are found in depleted domains. The genome was partitioned into 5-kbp non-overlapping windows, and those depleted of nucleosomes selected (determined as in Figure 2) and compared to the location of p65 binding sites (determined using ChIP-seq data obtained 30 min post-stimulation). By 10 min, 74,486 nucleosome-depleted windows appear, after 30 min 288,377 such windows develop (21,788 of which are also seen at 10 min). By 30 min, 8,554 p65 peaks are seen, but only 244 and 1,318 overlap (≥25% of sequence) with the 10- and 30-min nucleosome-depleted windows, respectively. (B) Nucleosome-depleted p65-containing windows are predominantly intragenic. Bar graphs give the fraction of nucleosome-depleted windows or p65 peaks (0, 10, 30 min) coinciding with regions lying within or outside annotated genes (blue - intragenic; grey - intergenic), or ±1 kbp from the transcription start site (purplr - promoter). (C) Browser tracks illustrating changes in nucleosome occupancy (log₂ fold-changes determined using 5-kbp non-overlapping windows as in Figure 2) in a 1-Mbp locus on chromosome 14 (TNFα-responsive genes - red, non-responsive - blue); p65 ChIP-seq tracks (0, 10 and 30 min post-TNFα; vertical axes - reads/million) are also shown. ChIP-seq, chromatin immunoprecipitation coupled to high-throughput sequencing; kbp, kilobase pair; TNFα, tumour necrosis factor alpha.