KDM6A facilitates Xist upregulation at the onset of X inactivation

Abstract

X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. Here, we investigate the role of KDM6A in the regulation of Xist. We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a. This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6a knockout results in aberrant overexpression of genes from the Xi after differentiation. KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist. These results indicate that KDM6A plays a role in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation.

Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation

“…Indeed, two recent studies have implicated the role of two X-linked but XCI-escaping histone demethylases, KDM5C/JARID1C and KDM6A/UTX, implicated in sexual differentiation (see review [52]) with opposing roles in enhancing Xist expression [21,53]. While KDM5C is an H3K4 demethylase, KDM6A is an H3K27 demethylase [54,55].…”

“…A recent preprint shows how another escaping gene, Kdm6a, might be involved in Xist expression regulation. Kdm6a KO ESCs exhibit female-specific impaired differentiation in vitro, decreased Xist expression levels with a concomitant reduction in Xist clouds, and impaired silencing of X-linked genes [53,56]. The authors propose a model where a double dosage of KDM6A in ESCs leads to H3K27me3 removal from the Xist promoter region, allowing for its upregulation.…”