Fig. 3: Assignment of the parental origin of the allele-specific contacts. | Nature Communications

Fig. 3: Assignment of the parental origin of the allele-specific contacts.

From: Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects

Fig. 3

a Sequencing read of a single clone of 3C-PCR product between H19-ICR and OREG0020670 near the KRTAP5-6 gene showed that it contains G allele (marked with green arrow) of H19-ICR (rs113013264) and −C/A/G allele (marked with blue arrows) of OREG0020670 (rs111402257/rs4752741/rs4752742). The sequencing read is from the reverse strand for H19-ICR and from the forward strand for OREG0020670. Red arrows show contact sites. Sequencing results of eight additional clones of this 3C-PCR product is shown in Supplementary Fig. 11. b Key features of OREG0020670. Dark gray: euchromatin. Light grey: heterochromatin. Previously and newly identified CTCF sites22 are marked by small boxes. Enlarged bar graph represents the CpG methylation status in this region. Pink: CTCF motif (see Supplementary Figs. 6 and 14). Blue: methylated region containing SNPs rs111402257, rs4752741 and rs4752742. Purple: unmethylated region. Yellow: Variable methylated region without strong allelic specificity. Red: Differentially methylated region with allelic specificity. Green: methylated region. The DNA sequence (hg19 chromosome 11: 1715431–1716230) is shown in detail in Supplementary Fig. 6.

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