FIGURE 6.

Recruitment and exclusion of p65 by dex is associated with distinct effects on RNAPII occupancy and differential enrichment for dimeric GR binding sites. A, scaled Venn diagram depicting the effect of the addition of TNF on dex-regulated occupancy of GR (top) in comparison to the effect of dex on TNF-regulated p65 occupancy. Numbers represent unique genes associated with sites of occupancy. B, distribution of relative local RNAPII occupancy (TNF + dex compared with TNF alone, expressed as log₂ of the occupancy ratio) at sites in which TNF + dex increased p65 occupancy (top) or decreased p65 occupancy (bottom) relative to TNF treatment alone. C, frequency distributions of maximal predicted GR binding affinities (on a log_e scale) within p65 binding regions in which p65 occupancy was increased (black) or decreased (red) by TNF + dex co-treatment versus TNF alone, within GR binding regions in which GR recruitment was increased with dex versus veh (green) or increased with TNF + dex versus dex alone (purple). The blue line shows the distribution of maximal calculated affinities within randomly shuffled sequences from the data set corresponding to the black line. Colored arrowheads indicate mean predicted GR binding affinities within corresponding subsets.