Fig. 3

Effects of imprinting domains on neighbouring loci and allele-specific compartment differences in normal cells. a An example of cross-TAD associations from an imprinted gene region. The subtraction matrix at the H19-KCNQ1 locus with allele-specific loops in H1-hESC demonstrating cross-TAD association between KCNQ1 region to NUP98 and RRM1 which are allele-specifically expressed (ASE), but not known to be imprinted. Gene density is shown in blue below the CTCF track, with imprinted genes below, and genes with ASE below. b Examples of allele-specific compartmentalization at SNRPN and DLK1-DIO3 loci. The diploid contact matrix (10kb resolution) with a Cscore below (blue for B-compartment, red A-compartment), followed by TAD insulation score, CTCF track, imprinted genes, and ASE genes. Adjacent to the diploid matrices are the haplotype phased allele-specific matrices (A1 and A2). Note the allele-specific differences in the Cscore track between A1 and A2 alleles at both loci. See Additional file 2: Fig. S6 for a comparison of the other cell lines, and subtraction matrices. c Allele-specific cross-TAD associations and additional TAD domains enriched for allele-specific associations near the DLK1-DIO3 locus. Subtraction matrices, SNP densities, allele-specific loops, imprinted and ASE genes are as described. The DLK1-DIO3 domain in H1-hESC and GM12878 forms several cross-TAD associations and has weak TAD boundaries. In H1-hESC several genes adjacent to the imprinted domain have allele-specific expression. In GM12878, a nearby TAD (labelled v-TAD) has stronger enrichment for allele-specific associations than DLK1-DIO3 locus