Studies in the mouse have shown that dosage compensation of sex chromosomes through X-chromosome inactivation (XCI) is required for the growth of extra-embryonic tissues and embryo development. The species specificity in mechanisms and timing leading to XCI during early embryogenesis, however, left the key question of the interdependence between XCI and human development open.

Here, we use the differentiation of human naïve pluripotent stem cells to trophoblast stem cells and extraembryonic mesoderm cells to investigate the role of XIST and XCI in the process.

We find that both cell types initiate XCI concomittantly with the appearance of lineage specific markers. The inactive X chromosome present in these cells, however, displays an atypical chromatin state when compared with the inactive X found in primed human embryonic stem cells, not associated with classical heterochromatin markers. We demonstrate that extraembryonic specification and XCI are kinetically and functionally linked. Using loss-of-function approaches, we formally prove that XIST is required for human XCI establishment. We also reveal that XCI is not required for neither naïve pluripotency exit nor for induction of lineage-specific markers. However, proper XCI is essential for the survival of human female extraembryonic cells.

Our work highlights the importance of X-chromosome gene dosage control for the proper specification of extraembryonic cells, which suggests important consequences for human reproductive biology.