Relationship between androgen receptor binding and DNase I hypersensitivity. (a) Overlap of each ChIP-seq AR binding peaks with poised LNCaP DHS (regions that are DHS sites in both LNCaP and LNCaP-induced) and LNCaP-induced only DHS sites. AR binding sites not overlapping a DHS site are represented in black. Common Myc and CTCF binding sites are shown as control. (b) Overlap of ChIP-seq peaks is shown at different thresholds of DNase-seq enrichment ('DHS sites' representing regions of significant signal over background P < 0.05, 'Top 200k' representing the top 200,000 initial peaks showing enrichment over background, and 'Top 400k' representing all regions showing DNase-seq enrichment over background). Columns in various shades of blue show overlap with LNCaP DHS at different thresholds, and columns in various shades of red show overlap with LNCaP-induced DHS at different thresholds. Common Myc and CTCF binding sites  are included as control. (c) Overlap between ΔDNase regions and AR binding sites in the context of AR binding sites that overlap with DHS sites. Shown are data for All AR ChIP-seq intersect peaks. Region I represents AR binding sites in LNCaP DHS sites only, Region II contains AR binding sites in a region that is both a LNCaP DHS site and LNCaP-induced DHS site (poised), and Region III represents AR binding sites in a region that is only a LNCaP-induced DHS site. Bottom figure shows overlap with ΔDNase strict and loose gain as well as loose decreases. Each region of overlap (I, II, III) is indicated by a different shade of purple. (d) AR ChIP-seq binding scores for peaks overlapping and not overlapping DHS sites as measured by MACS. Starred data points denote significant differences in AR peak score (Mann-Whitney P-value < 0.001). (e) De novo motif analysis of regions containing an AR ChIP-seq peak (All AR Intersect) and very low DNase-seq signal (black bars in Figure 3B) reveals a motif closely matching that of the AR, with a noticeable variation in the typically degenerate region (black arrow). (F) De novo motifs identified in ΔDNase regions that do not overlap AR ChIP-seq peaks (All AR Intersect). AR: androgen receptor; CTCF: CCCTC-binding factor; DHS: DNase I hypersensitive; DNase-seq: DNase I hypersensitivity analysis coupled with high-throughput sequencing.
Tewari et al. Genome Biology 2012 13:R88 doi:10.1186/gb-2012-13-10-r88