Promoter-enhancer 3D circuitry. (A) Number of enhancer elements interacting with between zero and more than five promoters in ESCs and FLCs. (B) Example of highly connected (HC) enhancer (represented by purple rectangle) contacting multiple gene promoters in ESCs. (C) Numbers of unique and overlapping promoters interacting with highly connected enhancers in ESCs and FLCs. (D) Numbers of unique and overlapping highly connected enhancers in ESCs and FLCs. (E) Percentage of promoters in the separate expression categories that contact enhancers, highly connected (HC) enhancers, super-enhancers, and nonenhancer elements in ESCs. (F) Percentages of active promoters interacting with the nearest enhancer (on the linear genomic map), a more distally located enhancer, or skipping (at least) one enhancer in ESCs and FLCs, as illustrated by schematic on the right ([P] promoter; [E] enhancer). (G) Example of an active promoter (Ramp1) bypassing proximal enhancers (red arrows) in ESCs.
