Fig. 7

Intrachromosomal contacts at X-linked genes and at imprinted genes. a Distribution of maternal-to-paternal allelic contacts at autosomal genes and X-linked genes determined by DNase Hi-C at 40 kb resolution in mouse F1 brain in which the paternal autosomes and the Xi are from spretus. Compared with autosomal genes, X-linked genes show high maternal-to-paternal ratios, indicating less frequent contacts at silent genes on the Xi. b Violin plots show the distribution of maternal-to-paternal allelic contacts at maternally and paternally imprinted genes and at genes that escape XCI at 40 kb resolution in F1 brain. Compared with other autosomal genes paternally expressed imprinted genes have a lower maternal-to-paternal contact ratio as shown by a long tail. These genes are preferentially located on chromosome 7 and when they are removed from the analysis, the shape of the distribution changes (as shown by a shorter tail in Additional file 8). The chromosomal location of imprinted genes is indicated by dots color-coded to indicate the chromosome of origin. The distribution of maternal-to-paternal allelic contacts for genes that escape XCI differs from the rest of X-linked genes, reflecting a higher number of contacts at expressed alleles. Dotted lines indicate median ratios of maternal-to-paternal contacts at autosomal and X-linked genes. c Significant contacts are detected between the imprinted paternally expressed gene Peg3 and neighboring regions on the paternal allele. Allelic RNA-seq confirms Peg3 expression on the paternal allele. Allelic CTCF profiles show binding to the differentially methylated region (DMR) adjacent to Peg3 promoter region only on the paternal allele (arrow), presumably facilitating the formation of contacts between the Peg3 promoter region and the distant enhancer ECR18 (evolutionarily conserved region 18) [63]. The needle plot of contacts counts between a 40 kb window that overlaps Peg3 (grey bar) and nearby regions shows more interactions on the paternal (blue, Pat) than the maternal allele (pink, Mat). Genes with maternal or paternal expression are colored in pink or blue, non-imprinted genes in black, and non-expressed genes in grey. Contact regions showing significant allelic biases are marked by asterisks