Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Nucleic Acids Res. 2020 Jul 9;48(12):6699-6714. doi: 10.1093/nar/gkaa457.


Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / genetics
  • Chromatin / genetics*
  • DNA / genetics*
  • Genome / genetics*
  • Humans
  • RNA, Messenger / genetics
  • RNA, Untranslated / genetics*
  • RNA, Untranslated / isolation & purification
  • Transcription Factors / genetics
  • Transcription, Genetic*


  • Chromatin
  • RNA, Messenger
  • RNA, Untranslated
  • Transcription Factors
  • DNA