SMCX & Random X-inactivation

Lack of Xist RNA induction upon SMCX/KDM5C loss in mouse EpiLCs

When pluripotent female epiblast cells differentiate, one of their two X chromosomes is inactivated in a random manner. Despite much progress, the factors and mechanisms that cause random X-inactivation selectively in females remain obscure. We recently postulated that genes that escape X-inactivation function as dose-sensitive factors that induce X-inactivation selectively in females (Gayen et al., 2016). X-inactivation escapees are expressed from both X chromosomes in females, including from the otherwise inactivated X chromosome. As a result, the expression of X-inactivation escapees is higher in females compared to males.

We nominated the X-inactivation escapee Smcx / Kdm5c as a candidate inducer of Xist and thus of X-inactivation. KDM5C demethylates histone H3 di- and tri- methylated at lysine 4 (H3K4me2 and H3K4me3), which are chromatin marks associated with active gene expression. And, unlike many other escapees, Kdm5c escapes X-inactivation in both mouse and human, suggesting an evolutionarily conserved dose-dependent function.

In testing a role for KDM5C in X-inactivation, we found that KDM5C is indeed required for Xist RNA induction (in the image above, Xist RNA coating is seen as a green 'cloud', the Xist antisense RNA is detected as a green pinpoint, and RNA from the X-linked gene Pgk1 is in red). When mouse embryonic stem cells (ESCs) are differentiated into epiblast-like cells (EpiLCs), the absence of KDM5C results in a deficiency in Xist RNA induction. These and other results suggest that KDM5C lies at or near the top of the molecular hierarchy that causes X-inactivation selectively in females and not in males (see model below and Samanta et al., 2022 for more information).

Ongoing and future work aims to dissect the evolutionarily conserved, dose-dependent function of the histone demethylase KDM5C in inducing random X-inactivation in mammalian females via both in vitro and in vivo approaches. We also aim to inhibit KDM5C as a means to reactivate silenced X-linked genes, which has therapeutic implications for X-linked gene disorders in females (e.g, Rett Syndrome).

A model of KDM5C function in random X-chromosome inactivation