Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female -specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.

Automated summary

Developmental genes like Xist are regulated by complex cis regulatory landscapes, which decode multiple signals to establish specific expression patterns. In this study, functional enhancer elements of Xist were identified during random X inactivation. X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. A previously unannotated enhancer cluster associated with Xist-enhancing regulatory transcript, named Xert, was also discovered. The study helps to understand how multiple regulatory elements interact to generate complex expression patterns in mammals.