Extended Data Fig. 4: Related to Figure 4.

a. Correlation between differential HiChIP connectivity/hubness and differential gene expression in connectivity and differential gene expression in ESC and TSC cells (top) and TSC and XEN cells (bottom). R represents Spearman correlation identifies distinct groups of genes. We focus on the two most prominent groups: 3D-insensitive genes, defined as genes with differential connectivity >3 but no transcriptional changes (log2FC < 1 or >-1) and 3D-concordant genes for which connectivity and expression changes (log2FC > 1 or <-1) positively correlate (Supplementary Table 5). b-e. Gene ontology analysis depicting the most significant biological processes enriched in the 3D concordant and 3D-insensitive genes in each pairwise comparison (ESC vs TSC and TSC vs XEN) as defined in (a). All genes in A compartments were used as background. For further details see also Supplementary Table 3. f. Comparison of connectivity, gene expression levels as well as H3K27ac and ATAC CPM levels between ESC and TSC cells (left) and TSC and XEN cells (right) at promoters of 3D-concordant (n = 1818 for ESC/TSC and n = 1108 for TSC/XEN) and 3D-insensitive genes (n = 2637 for ESC/TSC, n = 2230 for TSC/XEN) as defined in (a). Insensitive genes show higher levels of connectivity, H3K27ac, ATAC and expression in both cell types. X-axis indicates cell type (T = TSC, E = ESC, X = XEN). Two-sided Wilcoxon rank sum test was used for all comparisons with p > 0.05 indicating significance. (Supplementary Table 8). Note: all statistics are provided in Supplementary Table 8.