Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells

In this study, we have explored the role of Xist and DNA methylation in the maintenance of X-linked gene silencing in extraembryonic endoderm and epiblast stem cells. We show that only a subset of genes are dependent on Xist and DNA methylation to maintain their inactive state. Moreover, we show that the reactivation potential of X-linked genes upon loss of Xist is connected to the epigenomic states. Overall design: We performed RNA-seq in WT vs Xist knock out XEN and EpiSC to investigated the effect of loss of Xist upstream deletion in XEN cells. We also performed RNA-seq in Azacytidine treated XEN cells.