Fig. 5

LAD dynamics are not caused by transcriptional effects of CTCF and cohesin perturbation. A Overview of RNA-seq results for time courses of CTCF depletion and cohesin perturbation, showing differentially expressed genes (left panel) and log₂-fold changes (right panel) compared to 0 h. RNA-seq data in PT, RAD21, and WAPL clones are from ref. [26] B Comparison between the observed overlap in differentially expressed genes (left panel), versus a random overlap in differentially expressed genes (right panel). Only active genes (FPKM > 1) were considered for this comparison. C Distribution of LAD differences classified by the presence of up- and downregulated genes. LADs overlapping both up- and downregulated genes were excluded. Only conditions with at least 50 differentially expressed genes and available gene expression and pA-DamID data are shown. A Wilcoxon test was used to test for statistical significance, followed by Benjamini–Hochberg multiple testing correction (an asterisk denotes a p-value < 0.05)