X-chromosome inactivation in human iPSCs provides insight into escape-regulated gene expression

Epigenetic variation in the X chromosome inactivation (XCI) of human induced pluripotent stem cells (hiPSCs) can impact their ability to accurately model biological sex biases. However, the gene-wise landscape of escape from XCI remains unresolved in female hiPSCs. To characterize the patterns of escape from inactivation, we performed a systematic survey of allele specific expression (ASE) in 165 female hiPSC lines. The analysis revealed that the escape from XCI was non-random and affected primarily genes that escape also in human tissues. However, individual genes and cell lines varied in the frequency and degree of escape. The escape increased gradually after modest decrease of XIST in cultures, whose loss is commonly used to mark lines with eroded XCI. We identified three clusters of female lines at different stages of XCI. The increased degree of escape from XCI amplified female-biased expression and reduced male-female differences in genes with male-biased expression in the X chromosome. In autosomes, the increased escape modified genuine sex differences in a dose-dependent way suggesting that escape from XCI directly regulated autosomal gene expression. The variation in escape was sufficient to compensate for a dominant loss of function effect in several disease genes. The study presents a comprehensive view of escape from XCI in hiPSCs and emphasizes the need to monitor the XCI status at gene level for disease modeling. It further suggests that the uncommon and variable escape in hiPSCs can provide insight into X chromosome’s role in regulating gene expression and sex differences in humans.