Extended Data Fig. 3: Validation of enhancer-promoter multiplication via luciferase assays and modeling gene transcription as a function of intrinsic promoter activity and enhancer inputs.
From: Compatibility rules of human enhancer and promoter sequences
a. ExP luciferase reporter construct. Seven enhancer fragments, with flanking polyadenylation signals, were cloned upstream of five promoter fragments and measured via the dual luciferase assay. b. Autonomous promoter activity of ExP luciferase (average luciferase signal of promoter with negative control) for 5 promoter sequences derived from 3 genes (MYC, PVT1, CCDC26). Error bars are 95% CI from 6 (MYC) or 4 (all other promoters) biological replicates. c. Enhancer activation (luciferase signal versus negative control sequence in the enhancer position) of seven enhancers across five promoter fragments. Error bars are 95% CI from 6 (MYC) or 4 (all other promoters) biological replicates. d-f. Gene transcription (y-axis): PRO-seq read counts in the gene body. a. Promoter Activity (x-axis, left): Intrinsic promoter activity, as measured by ExP STARR-seq. b. Enhancer Input (x-axis, center): enhancer activity (based on measurements of H3K27ac and DHS in the genome) multiplied by enhancer-promoter contact (based on Hi-C measurements), summed across all putative enhancers (DHS peaks) within 5 Mb of the gene promoter (excluding the promoter’s own peak), weighted by HiC contact as in the ABC Model22. c. Promoter Activity x Enhancer Input (x-axis, right). Labels: gene symbols for 741 promoters with sequence activity estimates from ExP STARR-seq and enhancer input estimates from ABC. Dotted lines: Line of best fit from linear regression in log2 space.
