Fig. 3

Differential CR occupancy, chromatin landscape, and Pol II occupancy of bound and unbound RSINE1 elements. A ChIP-seq signal for each CR across circadian time (CT), centered at CR associated RSINE1 elements (n = 328, top) and a randomly selected set of 328 RSINE1 elements which fall within open chromatin regions as defined by DNase-seq but are not associated with CR binding (n = 328, bottom). Heatmaps are centered at the middle of each element in positive orientation, extend 750 bp in each direction, and are sorted by mean signal intensity across all rows for a given CR. B DNase-seq signal over Zeitgeber time (ZT). Regions, sorting, and centering as in A. C H3K27Ac ChIP-seq signal over Zeitgeber time (ZT). Regions, sorting, and centering as in A. D Pol II ChIP-seq signal over Zeitgeber time (ZT). Regions, sorting, and centering as in A. In all panels, color scaling is relative to min-max signal within each block of heatmaps. Trace above heatmaps is the average signal in each class