Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing

PLoS One. 2015 Apr 13;10(4):e0123387. doi: 10.1371/journal.pone.0123387. eCollection 2015.

Abstract

Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and RNA sequencing (RNA-Seq), to perform a non-biased search for RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured using an engineered DNA-binding molecule such as a transcription activator-like protein. Subsequently, RNAs that interact with the target genomic regions are purified and sequenced. The RNAs detected by enChIP-RNA-Seq contained known telomere-binding RNAs, including the telomerase RNA component (Terc), the RNA component of mitochondrial RNA processing endoribonuclease (Rmrp), and Cajal body-specific RNAs. In addition, a number of novel telomere-binding non-coding RNAs were also identified. Binding of two candidate non-coding RNAs to telomeres was confirmed by immunofluorescence microscopy and RNA fluorescence in situ hybridization (RNA-FISH) analyses. The novel telomere-binding non-coding RNAs identified here may play important roles in telomere functions. To our knowledge, this study is the first non-biased identification of RNAs associated with specific genomic regions. The results presented here suggest that enChIP-RNA-Seq analyses are useful for the identification of RNAs interacting with specific genomic regions, and may help to contribute to current understanding of the regulation of genome functions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Line
  • Cell Line, Tumor
  • Chromatin Immunoprecipitation*
  • Genetic Engineering
  • Humans
  • In Situ Hybridization, Fluorescence
  • Mice
  • Molecular Sequence Data
  • RNA / genetics
  • RNA, Untranslated / genetics*
  • Sequence Analysis, RNA*
  • Telomerase / genetics
  • Telomere / ultrastructure*

Substances

  • RNA, Untranslated
  • telomerase RNA
  • RNA
  • Telomerase

Associated data

  • GEO/GSE60425

Grant support

This work was supported by Takeda Science Foundation (T. F.), the Asahi Glass Foundation, the Uehara Memorial Foundation (H. F.), the Kurata Memorial Hitachi Science and Technology Foundation (T. F. and H. F.), Grant-in-Aid for Young Scientists (B) (#25830131) (T. F.), Grant-in-Aid for Scientific Research (C) (#26430133) (R. O.), Grant-in-Aid for Scientific Research on Innovative Areas "Cell Fate" (#23118516) (T. F.), "Transcription Cycle" (#25118512), "Genome Support" (#221S0002) (H. F.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and Applied Research for Innovative Treatment of Cancer from the Ministry of Health, Labour and Welfare (R. O.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.