Fig. 6

Complex patterns of imprinting at the ZNF331 and NAA60/ZNF597 loci revealed by phasing hundreds of transcribed SNVs. a Isoform-specific imprinting of ZNF331 has been previously reported [24, 27] where the longer isoform has biallelic expression in human LCLs, while the shorter isoforms have paternal expression. Isoforms expressed from the proximal promoter (boundaries indicated by green arrows under gene plot) show biallelic expression (left boxplot), while longer isoforms of the gene (boundaries indicated by the blue arrows) show strong paternal expression bias (right boxplot). Thus, depending on the position of the observed heterozygous SNVs within the ZNF331 gene, an individual may show different patterns of allelic bias. b Parental expression bias at NAA60/ZNF597, a complex locus that contains multiple overlapping imprinted and non-imprinted genes. The longest annotated isoform of NAA60 overlaps the imprinted gene ZNF597, and also the biallelically expressed genes, ZSCAN32, ZNF174, and LA16c-306E5.3. Considering SNVs within the boundaries of ZSCAN32 and LA16c-306E5.3 (regions defined by the green arrows) yields no evidence of imprinted expression, even though these are also contained within the longest annotated isoform of NAA60. However, considering SNVs located within the UGFs that uniquely describe ZNF597 (defined by red arrows) or NAA60 (defined by purple arrows) reveals almost exclusive expression from the maternal allele for these two genes. In the upper gene plots, each dot represents a single heterozygous SNV, which are colored to indicate the allelic ratio of the overlapping reads. Box plots show aggregate maternal and paternal read counts per individual