FIGURE 1. Dominant effect of chromatin accessibility on GR occupancy patterns.
(a–b) Examples of DNaseI sensitivity and GR occupancy patterns in relation to dexamethasone exposure (see Supplementary Figure 2a–c for additional examples). Each data track shows tag density (150bp sliding window) from either DNaseI-seq or GR ChIP-seq, normalized to allow comparison across different samples (Online Methods). Green arrows mark sites of post-hormone GR occupancy in pre-existing DNaseI-sensitive chromatin (‘pre-programmed’ sites). Red arrows mark GR occupancy sites in pre-hormone inaccessible chromatin that result in post-hormone chromatin remodeling (‘re-programmed’ sites). Blue arrows mark hormone-induced DHSs not directly associated with GR occupancy (see also Supplementary Fig 4c). (c) Venn diagram summarizing global GR occupancy vs. chromatin accessibility landscape (~25M read depth) in mammary cells (Note: for legibility, GR circle shown at 5X scale). Most GR occupancy occurs within pre-hormone accessible chromatin. A small fraction of generally weak GR peaks (5.2% of total) are not associated with re-programmed or pre-programmed chromatin. (d) DNaseI sensitivity (tag density) pre-hormone (horizontal axis) vs. post-hormone (vertical axis). Colors match those used in panel (c). Black = pre-hormone accessible regions with no post-hormone GR occupancy. Blue = DNaseI-sensitive regions induced post-hormone without GR occupancy (see Supplementary Fig 4c). Green = pre-hormone DNaseI sensitive regions occupied by GR post-hormone (‘pre-programmed’ sites). Red = pre-hormone inaccessible chromatin remodeled by GR occupancy (‘re-programmed’ sites), resulting in marked alteration in DNaseI sensitivity. (see Supplementary Fig 4a–b).