RNA Interactions Are Essential for CTCF-Mediated Genome Organization

Mol Cell. 2019 Nov 7;76(3):412-422.e5. doi: 10.1016/j.molcel.2019.08.015. Epub 2019 Sep 12.


The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of 2 of its 11 zinc fingers that are not required for CTCF binding to its cognate DNA site: zinc finger 1 (ZF1) or zinc finger 10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus the ability to insulate chromatin domains and to mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.

Keywords: CTCF; RNA binding; RNA deficient-mutants; TADs; chromatin domains; chromatin loops; chromatin organization; gene expression; transcriptional inhibition.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor / chemistry
  • CCCTC-Binding Factor / genetics
  • CCCTC-Binding Factor / metabolism*
  • Cell Line
  • Chromatin / chemistry
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Mice
  • Mouse Embryonic Stem Cells / metabolism*
  • Mutation
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*
  • Structure-Activity Relationship
  • Transcription, Genetic
  • Zinc Fingers


  • CCCTC-Binding Factor
  • Chromatin
  • Ctcf protein, mouse
  • RNA