Delayed DNA replication in haploid human embryonic stem cells

Abstract

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X chromosome in haploids, consistent with the lack of X chromosome inactivation. Surprisingly, we also identified 21 autosomal regions that had dramatically delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also under-replicated in polyploid placental cells. The same delays were observed in female ESCs with two active X chromosomes, suggesting that increased X chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication. HighlightsO_LIDNA replication timing of haploid ESCs profiled by WGS C_LIO_LIExtreme replication timing delays in haploid ESCs at unique genomic regions C_LIO_LIReplication delays associate with X-chromosome dosage in multiple systems C_LIO_LIReplication delayed regions correspond to underreplication in mouse polyploid cells C_LI