NIPBL and WAPL regulate the expression of unique and shared sets of genes.

(A) The log2(fold change) of genes after NIPBL knockdown versus their significance. DEGs are in green (999 up, 878 down) and non-significantly changed genes (nonDEGs, adjusted p-value > 0.01) are in grey. Average read density over genes from transcriptional start site (TSS) upregulated (middle) or downregulated (right) after NIPBL knockdown. (B) The log2(fold change) of genes after WAPL knockdown versus their significance. DEGs are in purple (910 up, 1022 down) and nonDEGs (adjusted p-value > 0.01) are in grey. Average read density over genes from TSS upregulated (middle) or downregulated (right) after WAPL knockdown. (C) Venn diagram of the number of NIPBL, WAPL, and shared DEGs. (D) Percentage of up, down, NIPBL, WAPL, or nonDEGs with a TSS within 5kb of a loop anchor. Fisher’s exact test compared to nonDEGs, **** p < 0.0001, *** p = 0.0002. (E) Distance from each NIPBL DEG TSS to the nearest loop anchor versus the fold change of the gene. Spearman correlation, p = 0.0018. (F) Distance from each WAPL DEG TSS to the nearest loop anchor versus the fold change of the gene. Spearman correlation, p = 0.037.