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

Mol Cell. 2022 Jan 6;82(1):190-208.e17. doi: 10.1016/j.molcel.2021.11.023. Epub 2021 Dec 20.


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.

Keywords: CRISPR screens; CRISPRi; X-chromosome inactivation; Xert; Xist; chromatin modifications; enhancers; epigenetics; lncRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation
  • Cell Line
  • Enhancer Elements, Genetic*
  • Female
  • Gene Expression Regulation, Developmental
  • Genetic Loci*
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Mouse Embryonic Stem Cells / metabolism*
  • Promoter Regions, Genetic*
  • RNA, Long Noncoding / genetics*
  • Up-Regulation
  • X Chromosome Inactivation*
  • X Chromosome*


  • RNA, Long Noncoding
  • XIST non-coding RNA