Fig. 3

Allele-specific sub-TAD organization of the Dlk1-Dio3 domain. a 4C-seq signal for the IG-DMR viewpoint in a 300-kb region around Dlk1-Meg3 on the maternal (red) and paternal (blue) chromosome in hybrid ESCs. The ratio of maternal/paternal interactions is provided in between. CTCF ChIP-seq signal is indicated below, with the arrow pinpointing the Meg3 DMR. Fosmid probes, positions of the viewpoints (see b), and the span of the maternal Dlk1-Dio3 sub-TAD are indicated above. b Distribution of 4C-seq signal for indicated viewpoints in the Dlk1-Meg3 sub-TAD (top) and the combined Dlk1-Meg3 and Mirg-Dio3 sub-TADs (bottom). c 3D DNA-FISH distance measurements with fosmid probes (see a) reveal similar distances between both sides of the Dlk1-Meg3 sub-TAD in mono-parental ESCs. d Allele-specific DNA-RNA FISH with combined fosmids and Meg3 RNA probes (MS2 sequences) in hybrid ESCs. Images show representative cells. Scale bars, 2 μm. e DNA-RNA FISH distance measurements (see f) reveal a larger distance between Dlk1 and Dio3 on the maternal chromosome. f 4C-seq signal for the IG-DMR viewpoint across the entire Dlk1-Dio3 TAD. Fosmid probes and the span of the sub-TADs (red box: Dlk1-Meg3 sub-TAD; see a) are indicated above. g Schematic representation of allele-specific CTCF-structured sub-TAD organization at the Dlk1-Dio3 domain. CTCF clusters (banners), allele specifically expressed genes (triangles), and reported regulatory elements (hexagons) are indicated