Fig. 5

Loss of Esrrb abrogates MIR enhancers. A Schematic illustration of the experimental system and strategy used for studying ESRRB-mediated and enhancer-related loops. H3 K27ac HiChIP maps were produced to characterize the interactome changes following Esrrb knockdown using shRNA system (Esrrb sh1 or Esrrb sh2). Empty vector (shCon) was used as control. The effect of H3 K27ac loop loss toward ESRRB-bound MIR interacting genes was examined. B Number of H3 K27ac-mediated chromatin loops at ESRRB-bound MIRs before and after Esrrb knockdown. C GO-terms enrichment of genes nearby ESRRB-bound MIRs with H3 K27ac loop loss. D WashU browser visualization of H3 K27ac loop loss around ESRRB-bound MIRs that interact with Klf5, Trim25, or Esrrb after Esrrb knockdown. H3 K27ac HiChIP signal and loops were shown in the tracks. E Distribution of H3 K27ac-mediated chromatin loops at super-enhancers (SEs) in control and Esrrb knockdown conditions. The boxplot summarizes the distribution of the number of loops and displays the median value for each group. F GSEA showing the expression change of SE-associated genes upon Esrrb knockdown in ESCs. For x-axis, genes were ranked by the expression fold change