Extended Data Figure 10: Stable enhancer loops prefigure gene expression and are associated with paused Pol II.
From: Enhancer loops appear stable during development and are associated with paused polymerase
Interaction map at three known Pol II paused genes: dve (a), Rx (b) and CG6959 (c). Top to bottom: Pol II signal (RPGC) in whole embryo at 2–4 h (orange)48, GRO-seq signal in whole embryo at 2–2.5 h (plus strand, red; minus strand, blue)28, RNA-seq signal (RPKM) in whole embryo at 2–4 h and 6–8 h (black)9, 4C interaction map (viewpoint, red arrowhead) in whole embryo at 3–4 h (purple) and 6–8h (dark blue). The ratio between whole embryo 3–4 h and whole embryo 6–8 h 4C signal is plotted in between in red. Significant 4C interactions and known enhancers are indicated. WE, whole embryo. Note, dve and Rx are transcribed on the plus strand, whereas CG6959 is transcribed on the minus. In each case, the enhancer–promoter interactions, Pol II occupancy in the absence of full-length transcript production (indicative of Pol II pausing56) and short nascent RNA transcription are already present at the promoter at 2–4 h, whereas the gene becomes highly expressed at 6–8 h. As the viewpoint in c is located 80 kb away from the promoter of CG6959, a zoomed-in view of the promoter is shown for clarity.
