Fig. 2

Imprinting control region (ICR) conformation at the Beckwith-Wiedemann syndrome locus impact differently on chromatin conformation. a Direct influence of the ICR in structuring local allele-specific chromatin conformation at the IGF2-H19 locus, in GM12878, IMR-90 and H1-hESC. Denoised subtraction matrices show that the CTCF regulated H19-DMR (arrow) subdivides the region (10kb resolution, blue areas correspond to A1, paternal allele, red areas to A2, maternal allele). Below the matrices we have the SNP density, and allele-specific loops, generated by Peakachu (red maternal, blue paternal), that corresponds to maternal and paternal expression of H19 and IGF2 respectively. The color of loops matches the underlying value of the subtraction matrix. The lower panels represent the viewpoint interaction traces for each cell line showing interactions between the H19-DMR and loci 400kb in both directions (blue trace A1, paternal, orange A2, maternal). The H19-DMR is methylated on the paternal allele in normal cells. b Indirect influence of the ICR in structuring local allele-specific chromatin conformation at the KCNQ1 locus, in GM12878, IMR-90 and H1-hESC. Subtraction matrices and viewpoint interaction traces as in a above but focused on the KCNQ1 locus and the KvDMR ICR (arrow), normally methylated on the maternal allele. Subtraction matrices and the allele-specific loops below display variable structural effects on chromatin conformation by the KvDMR. The viewpoint interaction traces mostly show weak biallelic interaction traces for the KvDMR associations. The CTCF site highlighted with an * is “region 3,” previously been shown to be important for allele-specific (maternal) expression of KCNQ1 [21]