Characterization of the RNA content of chromatin

Genome Res. 2010 Jul;20(7):899-907. doi: 10.1101/gr.103473.109. Epub 2010 Apr 19.


Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Animals
  • Cell Line
  • Chromatin / chemistry*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Conserved Sequence
  • DNA, Intergenic / genetics
  • Evolution, Molecular
  • Gene Expression Regulation
  • High-Throughput Screening Assays / methods
  • Humans
  • Introns / genetics
  • Mammals / genetics
  • RNA / analysis*
  • RNA / isolation & purification
  • RNA, Untranslated / genetics
  • RNA, Untranslated / physiology
  • Sequence Analysis, DNA / methods


  • Chromatin
  • DNA, Intergenic
  • RNA, Untranslated
  • RNA

Associated data

  • GEO/GSE21227