Fig. 2

Allele-specific sub-TAD organization of the Igf2-H19 domain. a 4C-seq signal for the H19 DMR viewpoint in the Igf2-H19 TAD on the maternal (red) and paternal (blue) chromosome in mono-parental ESCs. The ratio of maternal/paternal interactions is provided in between, with significant differences in both replicates, as determined by FourCSeq, indicated below [25]. CTCF ChIP-seq signal is indicated below, with the arrow pinpointing the H19 DMR. Reanalyzed Hi-C signal [11], fosmid probes, the position of the viewpoint, and span of maternal sub-domains are indicated above. b Examples of 3D DNA-FISH with fosmid probes in the Igf2-H19 TAD (see a). Images show representative cells in mono-parental ESCs. Scale bars, 2 μm. c 3D DNA-FISH distance measurements in mono-parental ESCs reveal a smaller distance between the mHIDAD and H19 probes on the maternal chromosome. d Directionality of 4C-seq signal for indicated viewpoints in the 5′ and 3′ sub-domains (see a). e 4C-seq line graphs for two bi-allelic CTCF clusters (viewpoint 1: cluster centromeric from the Syt8 gene; viewpoint 2: cluster in Lsp1 gene). Arrows indicate increased allele-specific signal at the H19 DMR (maternal) or telomeric from the Igf2 gene (paternal). f Schematic representation of allele-specific CTCF-structured sub-TAD organization at the Igf2-H19 domain. CTCF clusters (banners), allele specifically expressed genes (triangles), and reported regulatory elements (hexagon) are indicated