Deletion of lncRNA XACT does not change expression dosage of X-linked genes, but affects differentiation potential in hPSCs

Female human pluripotent stem cells (hPSCs) regularly show erosion of X chromosome inactivation featured by the loss of the long non-coding (lnc) RNA XIST and the accumulation of lncXACT. Here, we report that a common mechanism for the initiation of erosion depends on XIST loss but not XACT accumulation on inactive X chromosomes. We further demonstrate that XACT deletion does not affect X-linked gene dosage in eroded hPSCs and that aberrant XIST RNA diffusion induced by the CRISPR activation system is independent of the presence of XACT RNA. In contrast, the deletion of XACT results in the upregulation of neuron-related genes, facilitating neural differentiation in both male and eroded female hPSCs. XACT RNA repression by CRIPSR inhibition results in the same phenotype. Our study finds that XACT is dispensable for maintaining the erosion of X-lined gene repression on inactive X chromosomes but affects neural differentiation in hPSCs. [Display omitted] •XIST loss but not XACT accumulation on inactive X chromosome is common in XCI erosion•XACT deletion does not change expression dosage of X-linked gene in eroded female hPSCs•XACT regulates neural differentiation in both male and female hPSCs Motosugi et al. find that deletion of the lncRNA XACT in female hPSCs with the erosion of X chromosome inactivation does not alter the expression dosage of X-linked genes. However, XACT does regulate neuronal differentiation in both male and female hPSCs.