GLOBAL CHARACTERIZATION OF X CHROMOSOME INACTIVATION IN HUMAN PLURIPOTENT STEM CELLS

X chromosome inactivation (XCI) is an essential epigenetic dosage compensation process established during embryonic development of female mammals. Activation of the lncRNA XIST, which triggers XCI, occurs early during differentiation, therefore human pluripotent stem cells (hPSCs) are potentially a major model for studying this process. While XCI was extensively studied in mice, there are significant differences compared to humans. Previous studies demonstrated variable states of XCI in hPSCs, which are maintained after differentiation, thus impeding the use of these cells in therapeutic applications. These studies however focused on a limited number of cell-lines grown in the same lab. Here, we performed a large-scale characterization of XCI in 785 hPSCs from various sources, using RNA-sequencing. The analysis combined inputs on XIST expression, allelic polymorphism quantification and global expression levels of X-linked genes. These genome-wide evaluations enabled a sensitive and accurate classification of XCI state. We identify a striking difference between embryonic stem cells (ESCs) and induced PSCs (iPSCs) in their XCI landscape. Most iPSCs maintain the inactive X of their parental somatic cells, whereas ESCs silence the expression of XIST and upregulate distal regions of the X-chromosome. We suggest this to be the most significant epigenetic difference between ESCs and iPSCs. We further show that this erosion is slightly reduced upon differentiation, in a XIST-independent manner. Altogether, we propose a model in which XCI variations in hPSC lines are affected by epigenetic memory of their different parental sources, as well as by dynamic changes occurring during derivation and culture of hPSCs.