Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes

Cell. 2014 Feb 27;156(5):907-19. doi: 10.1016/j.cell.2014.01.042.

Abstract

Recent studies recognize a vast diversity of noncoding RNAs with largely unknown functions, but few have examined interspersed repeat sequences, which constitute almost half our genome. RNA hybridization in situ using C0T-1 (highly repeated) DNA probes detects surprisingly abundant euchromatin-associated RNA comprised predominantly of repeat sequences (C0T-1 RNA), including LINE-1. C0T-1-hybridizing RNA strictly localizes to the interphase chromosome territory in cis and remains stably associated with the chromosome territory following prolonged transcriptional inhibition. The C0T-1 RNA territory resists mechanical disruption and fractionates with the nonchromatin scaffold but can be experimentally released. Loss of repeat-rich, stable nuclear RNAs from euchromatin corresponds to aberrant chromatin distribution and condensation. C0T-1 RNA has several properties similar to XIST chromosomal RNA but is excluded from chromatin condensed by XIST. These findings impact two "black boxes" of genome science: the poorly understood diversity of noncoding RNA and the unexplained abundance of repetitive elements.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Nucleus / chemistry
  • Chromosomes, Mammalian / chemistry*
  • Euchromatin / chemistry*
  • Humans
  • Hybrid Cells
  • Interphase*
  • Long Interspersed Nucleotide Elements
  • Mice
  • RNA, Untranslated / analysis*
  • RNA, Untranslated / genetics
  • Repetitive Sequences, Nucleic Acid
  • Transcription, Genetic

Substances

  • Euchromatin
  • RNA, Untranslated