A protein assembly mediates Xist localization and gene silencing

Nature. 2020 Nov;587(7832):145-151. doi: 10.1038/s41586-020-2703-0. Epub 2020 Sep 9.


Nuclear compartments have diverse roles in regulating gene expression, yet the molecular forces and components that drive compartment formation remain largely unclear1. The long non-coding RNA Xist establishes an intra-chromosomal compartment by localizing at a high concentration in a territory spatially close to its transcription locus2 and binding diverse proteins3-5 to achieve X-chromosome inactivation (XCI)6,7. The XCI process therefore serves as a paradigm for understanding how RNA-mediated recruitment of various proteins induces a functional compartment. The properties of the inactive X (Xi)-compartment are known to change over time, because after initial Xist spreading and transcriptional shutoff a state is reached in which gene silencing remains stable even if Xist is turned off8. Here we show that the Xist RNA-binding proteins PTBP19, MATR310, TDP-4311 and CELF112 assemble on the multivalent E-repeat element of Xist7 and, via self-aggregation and heterotypic protein-protein interactions, form a condensate1 in the Xi. This condensate is required for gene silencing and for the anchoring of Xist to the Xi territory, and can be sustained in the absence of Xist. Notably, these E-repeat-binding proteins become essential coincident with transition to the Xist-independent XCI phase8, indicating that the condensate seeded by the E-repeat underlies the developmental switch from Xist-dependence to Xist-independence. Taken together, our data show that Xist forms the Xi compartment by seeding a heteromeric condensate that consists of ubiquitous RNA-binding proteins, revealing an unanticipated mechanism for heritable gene silencing.

Publication types

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

MeSH terms

  • Animals
  • CELF1 Protein / metabolism
  • Cell Line
  • DNA-Binding Proteins / metabolism
  • Female
  • Gene Silencing*
  • Heterogeneous-Nuclear Ribonucleoproteins / metabolism
  • Humans
  • In Situ Hybridization, Fluorescence
  • Male
  • Mice
  • Nuclear Matrix-Associated Proteins / metabolism
  • Polypyrimidine Tract-Binding Protein / metabolism
  • RNA, Long Noncoding / genetics*
  • RNA-Binding Proteins / metabolism*
  • X Chromosome Inactivation / genetics


  • CELF1 Protein
  • CELF1 protein, mouse
  • DNA-Binding Proteins
  • Heterogeneous-Nuclear Ribonucleoproteins
  • Nuclear Matrix-Associated Proteins
  • Ptbp1 protein, mouse
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • TDP-43 protein, mouse
  • XIST non-coding RNA
  • matrin-3 protein, mouse
  • Polypyrimidine Tract-Binding Protein