Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading

Science. 2021 Jun 11;372(6547):eabe7500. doi: 10.1126/science.abe7500.


X-inactive specific transcript (Xist) RNA directs the process of X chromosome inactivation in mammals by spreading in cis along the chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms of Xist RNA cis-confinement, we established a sequential dual-color labeling, super-resolution imaging approach to trace individual Xist RNA molecules over time, which enabled us to define fundamental parameters of spreading. We demonstrate a feedback mechanism linking Xist RNA synthesis and degradation and an unexpected physical coupling between preceding and newly synthesized Xist RNA molecules. Additionally, we find that the protein SPEN, a key factor for Xist-mediated gene silencing, has a distinct function in Xist RNA localization, stability, and coupling behaviors. Our results provide insights toward understanding the distinct dynamic properties of Xist RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Cell Nucleus / metabolism
  • Chromatin / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Embryonic Stem Cells
  • Gene Silencing
  • Mice
  • Microscopy
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • RNA Stability
  • RNA, Long Noncoding / biosynthesis
  • RNA, Long Noncoding / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Spatial Analysis
  • Transcription, Genetic
  • X Chromosome / metabolism
  • X Chromosome Inactivation*


  • Chromatin
  • Ciz1 protein, mouse
  • DNA-Binding Proteins
  • Nuclear Proteins
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • Spen protein, mouse
  • XIST non-coding RNA