Human Pluripotent Stem Cells with Distinct X Inactivation Status Show Molecular and Cellular Differences Controlled by the X-Linked ELK-1 Gene

•XaXa cells show high levels of apoptosis/differentiation in comparison to XaXi cells•Genes upregulated in XaXa cells are targets of the X-linked gene ELK-1•ELK-1 overexpression or downregulation mimic the phenotype of XaXa or XaXi cells•Differences between XaXa and XaXi cells are diminished at low oxygen levels

SummaryFemale human pluripotent stem cells show vast heterogeneity regarding the status of X chromosome inactivation. By comparing the gene expression profile of cells with two active X chromosomes (XaXa cells) to that of cells with only one active X chromosome (XaXi cells), a set of autosomal genes was shown to be overexpressed in the XaXa cells. Among these genes, we found significant enrichment for genes regulated by the X-linked transcription factor ELK-1. Comparison of the phenotype of XaXa and XaXi cells demonstrated differences in programmed cell death and differentiation, implying some growth disadvantage of the XaXa cells. Interestingly, ELK-1-overexpressing cells mimicked the phenotype of XaXa cells, whereas knockdown of ELK-1 with small hairpin RNA mimicked the phenotype of XaXi cells. When cultured at low oxygen levels, these cellular differences were considerably weakened. Our analysis implies a role of ELK-1 in the differences between pluripotent stem cells with distinct X chromosome inactivation statuses.

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