Fig. 6

The three regions escaping XCI colocalize with TADs as identified in ES_Tsix-stop ESCs. a–c Overview of the TADs present at regions 1, 2 and 3 [indicated with a box in (a), (b) and (c), respectively] in the female ES_Tsix-stop ESCs. In red, the interaction matrix used for TAD calling with domains indicated by dashed lines. The second row shows the spearman correlation between the 40 kb-binned Hi-C interaction matrices of the female ES_Tsix-stop and male J1 ESCs [51] (see “Materials and methods” for further details). The legend for genes that escape XCI or genes that are silenced is indicated in (a). Coloring of genes indicates escape in one or two NPC lines, respectively, while genes in black are X-inactivated in all NPC lines. Wdr45 and Slc35a2 are included as escape gene for *NPC_129-Xi as the contribution in gene expression from the Xi is >10 % (Table 1). Additional file 1: Figure S17 contains the same information as Fig. 6, but includes genes for which no allelic information was obtained (mainly due to low expression or the absence of polymorphic sites), as well as the interaction matrix in male J1 ESCs obtained from Dixon et al. [51] for comparison