Fig. 5

LXRs and PPARG maintain temporally distinct gene regulatory functions. a Cumulative distribution functions display the fraction of target gene promoters (y-axis) at different distance cutoffs to the nearest LXRA, LXRB, and PPARG binding event (x-axis). The nearest binding event to each gene promoter was used. Data for promoters of responsive up-regulated genes (green) and repressed (red) genes (adjusted p < 0.01, fold change cutoff of ±2) are shown. The background distribution using all gene promoters in the genome is also displayed (Bkgd, black). The top panel represents 2-h ChIP-seq data compared with 24-h RNA-seq data while the bottom panel compares 48-h ChIP-seq and RNA-seq data. For LXR data, GW3965 + T0901317 responsive genes are shown. Down-regulated curves are absent for 24-h GW3965 + T0901317 datasets as only one target gene was identified. b Cumulative distribution functions display the fraction of 48-h GW3965 + T0901317 repressed gene promoters (y-axis, adjusted p < 0.01, fold change cutoff of ±2) at different distance cutoffs to the nearest LXRA binding event (x-axis). LXRA binding events coincident with RNAP2 are in dark purple (+RNAP2), while LXRA sites devoid of RNAP2 occupancy are denoted in pink (-RNAP2). The background distribution using all gene promoters in the genome for sites overlapping with RNAP2 (+RNAP2 Bkgd, black) or for sites devoid of RNAP2 (-RNAP2 Bkgd, gray) is also graphed. The pie chart depicts the fraction of LXRA sites coincident with RNAP2 (green). c Cumulative distribution functions display the fraction of 48-h GW3965 + T0901317 repressed gene promoters (y-axis, adjusted p < 0.01, fold change cutoff of ±2) at different distance cutoffs to the nearest LXRB binding event (x-axis). LXRB binding events coincident with RNAP2 are in dark purple (+RNAP2), while LXRB sites devoid of RNAP2 occupancy are denoted in pink (-RNAP2). The background distribution using all gene promoters in the genome for sites overlapping with RNAP2 (+RNAP2 Bkgd, black) or for sites devoid of RNAP2 (-RNAP2 Bkgd, gray) is also graphed. The pie chart depicts the fraction of LXRB sites coincident with RNAP2 (green). d Read depth ratios (x-axis) of RNAP2 enrichment at LXRA binding sites (LXRA + RNAP2). Negative values highlight stronger enrichment under control culture conditions (DMSO; 0 h) while positive values denote stronger enrichment after 48 h of GW3965 treatment. e Read depth ratios (x-axis) of RNAP2 enrichment at LXRB binding sites (LXRB + RNAP2). Negative values highlight stronger enrichment under control culture conditions (DMSO; 0 h) while positive values denote stronger enrichment after 48 h of GW3965 treatment