Fig. 3

Deletion of the two CTCF-binding arrays in divergent orientations led to increase in inter-domain contacts. a We produced the three deletion alleles termed del1, del2 and del3, as depicted, which consecutively cover the whole intergenic region between Tfap2c and Bmp7. Note that del2 completely diminishes the two arrays of CTCF sites, TZ-L and TZ-R, while the other two delete the adjacent regions. The CTCF-binding sites in ES cells are depicted as in Fig. 2d. b–e 4C-seq plots from the VP-Fam209 (b), VP-Tfap2c (c), VP-Spo11 (d) and VP-Bmp7 (e). f–i The ratios of “invasion reads” to “control reads,” each mapped to the areas depicted by the red and black rectangles, respectively, in (b–e), were compared between different alleles, for each viewpoint. Each dot represents a replicate of differently prepared 4C-seq libraries from collection of cells. * indicates p < 0.05 by one-sided permutation test against the Hap allele. Note that del2 allowed the inter-domain contacts most among the three deletions for all of the viewpoints, although the size of the deletion is smaller than that of del1