Pluripotent stem cell–specific imprinted genes identified using human uniparental-induced pluripotent stem cells

Genomic imprinting is an epigenetic mechanism in which gene expression is determined by the parent of origin. Imprinted genes are crucial for mammalian growth and development, and mutations at imprinting sites can lead to developmental disorders and diseases. Therefore, identifying novel imprinted differentially methylated regions (DMRs) is essential for understanding imprinting mechanisms and their implications in human biology. This study aimed to identify new imprinted DMRs using parthenogenetic and androgenetic human induced pluripotent stem cells (PgHiPSCs and AgHiPSCs), derived from mature cystic teratomas and complete hydatidiform moles, respectively. Genome-wide DNA methylation profiling via DNA methyl-capture sequencing (MethylCap-seq) was used to identify candidate imprinted DMRs. Subsequent bisulfite sequencing validated the methylation status, and comparative analyses confirmed pluripotency-specific imprinting. We identified 26 novel imprinted DMRs and excluded 6 that exhibited the absence of allelic imbalance or the presence of potential confounding by expression quantitative trait locus. Among the remaining 20, the DMRs in DOCK4 and LYNX1 were validated. They had distinct imprinted methylation and expression patterns unique to pluripotent stem cells and absent in fibroblasts and normal adult tissues. These findings highlight the utility of uniparental iPSCs for discovering imprinted genes specific to the pluripotent state and provide insights into the epigenetic regulation of early human development.