A chromatin loop alters the frequency of enhancer-promoter interactions.

(A) Five sample conformations from polymer simulations with a 30 kb permanent loop (black) formed between two loop bases (orange) in a 1 Mb region of fiber. (B) Average heatmap (300 kb by 300 kb) for polymer simulations of the permanent, one-loop system, with a 30 kb loop (aggregated over 800,000 simulated conformations). Top and left edges show positions of the enhancer (yellow), promoter (blue), and loop bases (orange) for insulation and facilitation arrangements. (C) Schematics of E-P arrangements. (top) chromatin fiber without a fixed loop and with E-P genomic distance of 50 kb, as used to calculate expected (no-loop) contact frequencies (Methods). (middle) arrangement where insulation is observed, represented by the red “X”. (bottom) arrangement where facilitation is observed. (D) Contact frequency ratios (Methods) for insulation and facilitation arrangements with a 30 kb loop and 50 kb E-P genomic distance. Here and below, error bars indicate one standard deviation about the mean.