Escape from X inactivation is directly modulated by Xist non-coding RNA [multiclone]

X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with varying Xist levels. Overall design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a 129/Sv x CAST/EiJ cross). Clones from 21 cell lines were generated in three independent experiments. RNA-Sequencing was performed for each cell line. Using heterozygous variants between the two strains, allele-specific expression of X-linked genes was quantified together with Xist expression.