Fig. 6. Novel imprinting clusters and novel genes in known clusters.

a, b Close-up views of genomic features (genes, DMRs, allele-specific H3K27me3 and allele-specific TADs) for gene clusters containing published imprinted genes containing at least one nBsX gene (clusters 23-27) (a) and gene clusters containing only nBsX genes (clusters 28-32) (b). Red indicates maternal, and blue paternal allelic expression (genes quadrant; based on our data), maternal/paternal H3K27me3 (H3K27me3 quadrant; based on⁴³), maternal/paternal DMR (DMR quadrant; based on our data), maternal/paternal TAD (TAD quadrant; based on⁴²). Grey colour for specified genes indicates published imprinted genes for which parent-of-origin-specific expression was not confirmed; grey genes without gene names represent neighbouring genes not included in the cluster analysis. ncRNAs are indicated in italics. nBsX genes are indicated in bold. c Visualisation of chromosomal locations of imprinted genes and chromatin marks. Blastocyst DMRs are plotted as bars to the left in gold, known GL-DMRs are shown in blue. The density of tested regions (regions with reads in µWGBS) are plotted in grey. Parent-of-origin expression bias is shown on the right. nBiX and nBsX genes are plotted in gold and published imprinted genes in blue. The density of all robustly expressed genes is plotted in grey. All clusters of (a) and (b) and Supplementary Figs. 8a and b are indicated [blue, clusters 1–12 (published imprinted genes and at least one pubBsX gene); violet, clusters 13–22 (published imprinted genes with no evidence of parent-of-origin-specific expression in blastocysts); green, clusters 23–27 (published imprinted genes and containing at least one nBsX gene); yellow, clusters 28–32 (containing only nBsX genes)]. The locations of all allele-specific H3K27me3-associated promoters are indicated as red bands overlaid on the chromosome ideograms. Source data are provided as Source Data files.