Promoter and enhancer activities are positively correlated but quantitatively decoupled. (A) Mean promoter and enhancer activities across all promoter-derived and distal enhancer-derived tiles and the numbers of tiles with significant promoter or enhancer activities (FDR 0.1). (B) Mean promoter and enhancer activity as a function of the distance of the center of MPRA tiles to the nearest RefSeq TSS. Negative distances correspond to tile locations upstream of the TSS. (C) Mean promoter activity for tiles cloned into the MPRA promoter test in sense (566 tiles) versus antisense (467 tiles) orientations relative to their endogenous mRNA TSS. The genomic antisense TSS position depicts the approximate location of the endogenous antisense TSS, based on a median 180-bp distance between sense and antisense TSSs (Scruggs et al. 2015). (D) Enhancer activity versus promoter activity, with each dot corresponding to one tile. Each tile's activities are shown once for unstimulated and once for KCl-depolarized neurons. The area in which both activities fall above an empirical FDR of 0.1 is shown in gray. (E) The ratio of promoter-to-enhancer activities of tiles derived from promoter and distal enhancer loci (P-value from two-tailed Student's t-test). Error bars in A–C indicate SEM for n = 2 independent biological replications. Promoter and enhancer activities are defined as in Figure 2B.
