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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