XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells

Cell. 2024 Jan 4;187(1):110-129.e31. doi: 10.1016/j.cell.2023.11.033.

Abstract

X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

Keywords: X chromosome dampening; X chromosome inactivation; XIST; dispersed localization; dosage compensation; human pluripotent stem cells; lncRNA; polycomb-repressive complexes; sexual dimorphism; trans-acting.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Female
  • Gene Silencing
  • Genes, X-Linked*
  • Humans
  • Male
  • Mice
  • Pluripotent Stem Cells / metabolism
  • RNA, Long Noncoding* / genetics
  • X Chromosome* / genetics

Substances

  • RNA, Long Noncoding