Genomic imprinting is a special form of epigenetic modification of the genome in which gene expression is determined by parent-of-origin. Imprinted genes are important in normal fetal and placental development, and their dysregulation has been implicated in several important abnormalities, including intrauterine growth retardation. Although the phenomenon of genomic imprinting has been recognized for a quarter century, only about 160 imprinted genes total have been identified in humans and mice, the species most widely studied, despite strenuous efforts of many research groups around the world to identify more. Computational bioinformatic approaches aimed at predicting the imprinting status of genes have generated long lists of candidates, but few of those genes have yet been shown to be imprinted. We hypothesized that it should be possible to identify imprinted genes more easily in tissue samples from interspecies hybrids, in which there are more genetic differences between the maternal and paternal genome than in intraspecies matings. We chose to study gene expression in invasive trophoblast tissues from the reciprocal equine hybrids, the mule and hinny. There is evidence for differences in placental anatomy and physiology between mules and hinnies that is consistent with an imprinting origin. We used massively parallel Illumina short-read sequencing (RNA-seq) to examine parent-of-origin gene expression in the transcriptomes of chorionic girdle trophoblast samples from conceptuses of mule and hinny. Genes with parent-of-origin bias in their expression patterns were identified based on Single Nucleotide Polymorphism (SNP) differences in orthologous genes in the two parent species. Fourteen of these genes are known to be imprinted from studies of other species, and seven are novel. Using pyrosequencing, the biased parent-of-origin expression patterns for these genes were confirmed in mule and hinny placental tissue. The expression of a subset of these genes was examined in lymphocytes from mules and hinnies, and in this adult tissue the imprinted genes were expressed bi-allelically, as has been shown for some imprinted genes in humans. The novel and known imprinted genes of mule and hinny thus appear to be regulated like imprinted genes identified in other species. A substantial core of the imprinted genes identified in humans show similar imprinting patterns in mice, pigs, and cattle. Thus, it seems reasonable that some fraction of the new imprinted genes identified in interspecies equid hybrids would also be imprinted in humans and other mammals.
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