Fig. 1

DEGs and SEGs, and corresponding TADs. A Gene expression (GE) distribution for each three lineages: for all genes (top), DEGs (middle) and SEGs (bottom). B Violin plots showing distances in base pairs to the nearest gene (TSS of gene to TSS of neighbouring gene) in a gene set depending on GE level: genes not depending on GE threshold (ALL GE, left), and genes with GE log (RPKM) > 2 (right). DEGs (blue, all three lineage-specific DEGs combined) are significantly further away from their neighbours than SEGs (orange, Mann-Whitney test, p < 0.01). C DEG- and SEG-only TADS do not differ in size (Mann-Whitney p = 0.79), but SEG-only TADS have a significantly higher gene density (computed and normalised in a 100-kB window) than DEG-only TADs (Mann-Whitney p = 0.021). D Upset plot showing content of TADs made up exclusively of genes expressed in just ectoderm, endoderm or mesoderm (DEGs, green), solely of similarly expressed genes (SEGs, yellow) and TADs whose content is an intersection of any two or three of the four sets. The dominance of coloured bars on the top left shows that the majority of TADs contain either DEGs or SEGs, with minimal intersections. E Hi-C interaction maps showing a typical DEG-only TAD (left) and a representative SEG-only TAD (right). The TAD on the left contains a single DEG (Foxa2), whereas the map on the right shows 16 SEGs sharing the same TAD. Genes are denoted by blue boxes, accessible chromatin by red boxes and known enhancers by green boxes. Long orange rectangle at the left plot shows the borders of the TAD, while the area under the interaction map on the right plot shows the whole SEG-containing TAD