Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

Science. 2015 Jul 17;349(6245):10.1126/science.aab2276 aab2276. doi: 10.1126/science.aab2276. Epub 2015 Jun 18.


The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform "identification of direct RNA interacting proteins" (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors-including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers, and modifiers-that synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. Although Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / metabolism
  • Animals
  • Cell Cycle Proteins / metabolism*
  • Cells, Cultured
  • Chromatin Assembly and Disassembly
  • Chromosomal Proteins, Non-Histone / metabolism*
  • Cohesins
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / metabolism
  • Fibroblasts / metabolism
  • Gene Knockdown Techniques
  • Gene Silencing
  • Mice
  • Multiprotein Complexes / metabolism
  • Nucleic Acid Conformation
  • Proteomics
  • RNA Helicases / metabolism
  • RNA, Long Noncoding / metabolism*
  • X Chromosome / chemistry
  • X Chromosome / genetics
  • X Chromosome / metabolism*
  • X Chromosome Inactivation*


  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Multiprotein Complexes
  • RNA, Long Noncoding
  • XIST non-coding RNA
  • condensin complexes
  • Adenosine Triphosphatases
  • RNA Helicases

Associated data

  • GEO/GSE67516