Genome-wide assessment of imprinted expression in human cells

Abstract

Background: Parent-of-origin-dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine allelic expression across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families.

Results: We were able to validate 43% of imprinted genes with previous demonstration of compatible transmission patterns in LCLs and fibroblasts. In contrast, we only validated 8% of genes suggested to be imprinted in the literature, but without clear evidence of parent-of-origin-determined expression. We also detected five novel imprinted genes and delineated regions of imprinted expression surrounding annotated imprinted genes. More subtle parent-of-origin-dependent expression, or partial imprinting, could be verified in four genes. Despite higher prevalence of monoallelic expression, immortalized LCLs showed consistent imprinting in fewer loci than primary cells. Random monoallelic expression has previously been observed in LCLs and we show that random monoallelic expression in LCLs can be partly explained by aberrant methylation in the genome.

Conclusions: Our results indicate that widespread parent-of-origin-dependent expression observed recently in rodents is unlikely to be captured by assessment of human cells derived from adult tissues where genome-wide assessment of both primary and immortalized cells yields few new imprinted loci.

Figure 1

Examples of imprinted genes in Human genome. (a) Imprinted genes in both lymphoblasts and fibroblasts: GNAS is an example of an imprinted gene that has been previously described in the literature and has been confirmed in our study as well. (b) Imprinted genes in fibroblasts only: PLAGL1 is an example of tissue-specific imprinting (isoform 1). (c) Novel imprinted genes: ZDBF2 is an example of a novel imprinted gene. In each case, the figure shows all of the informative pedigrees. For the trios, the colors indicate the paternal allele (blue) and the maternal allele (red). For the three-generation pedigree the colors indicate which parental allele is inherited. The bars indicate which allele is overexpressed as well as the degree of overexpression.

Figure 2

Examples of imprinted genomic regions in fibroblasts. (a) Paternally expressed imprinted region on chr14 covering numerous non-RefSeq genes found downstream of the paternally imprinted DLK1 gene (was not informative in our samples). This region has been previously identified in mice and sheep. (b) Extension of imprinting with paternal expression downstream of the SNRPN/SNURF loci encompassing multiple non-RefSeq genes. (c) Maternally expressed imprinted gene ZNF597 with upstream imprinted isoform-specific NAT15.