Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

Georges St Laurent, Dmitry Shtokalo, Michael R. Tackett, Zhaoqing Yang, Tatyana Eremina, Claes R Wahlestedt, Silvio Urcuqui-Inchima, Bernd Seilheimer, Timothy A. McCaffrey, Philipp Kapranov

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

Background: The function of RNA from the non-coding (the so called " dark matter" ) regions of the genome has been a subject of considerable recent debate. Perhaps the most controversy is regarding the function of RNAs found in introns of annotated transcripts, where most of the reads that map outside of exons are usually found. However, it has been reported that the levels of RNA in introns are minor relative to those of the corresponding exons, and that changes in the levels of intronic RNAs correlate tightly with that of adjacent exons. This would suggest that RNAs produced from the vast expanse of intronic space are just pieces of pre-mRNAs or excised introns en route to degradation.Results: We present data that challenges the notion that intronic RNAs are mere by-standers in the cell. By performing a highly quantitative RNAseq analysis of transcriptome changes during an inflammation time course, we show that intronic RNAs have a number of features that would be expected from functional, standalone RNA species. We show that there are thousands of introns in the mouse genome that generate RNAs whose overall abundance, which changes throughout the inflammation timecourse, and other properties suggest that they function in yet unknown ways.Conclusions: So far, the focus of non-coding RNA discovery has shied away from intronic regions as those were believed to simply encode parts of pre-mRNAs. Results presented here suggest a very different situation - the sequences encoded in the introns appear to harbor a yet unexplored reservoir of novel, functional RNAs. As such, they should not be ignored in surveys of functional transcripts or other genomic studies.

Original languageEnglish
Article number504
JournalBMC Genomics
Volume13
Issue number1
DOIs
StatePublished - Sep 24 2012

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Untranslated RNA
RNA
Introns
Exons
RNA Precursors
Genome
Inflammation
Gene Expression Profiling

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

St Laurent, G., Shtokalo, D., Tackett, M. R., Yang, Z., Eremina, T., Wahlestedt, C. R., ... Kapranov, P. (2012). Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics, 13(1), [504]. https://doi.org/10.1186/1471-2164-13-504

Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. / St Laurent, Georges; Shtokalo, Dmitry; Tackett, Michael R.; Yang, Zhaoqing; Eremina, Tatyana; Wahlestedt, Claes R; Urcuqui-Inchima, Silvio; Seilheimer, Bernd; McCaffrey, Timothy A.; Kapranov, Philipp.

In: BMC Genomics, Vol. 13, No. 1, 504, 24.09.2012.

Research output: Contribution to journalArticle

St Laurent, G, Shtokalo, D, Tackett, MR, Yang, Z, Eremina, T, Wahlestedt, CR, Urcuqui-Inchima, S, Seilheimer, B, McCaffrey, TA & Kapranov, P 2012, 'Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells', BMC Genomics, vol. 13, no. 1, 504. https://doi.org/10.1186/1471-2164-13-504
St Laurent, Georges ; Shtokalo, Dmitry ; Tackett, Michael R. ; Yang, Zhaoqing ; Eremina, Tatyana ; Wahlestedt, Claes R ; Urcuqui-Inchima, Silvio ; Seilheimer, Bernd ; McCaffrey, Timothy A. ; Kapranov, Philipp. / Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. In: BMC Genomics. 2012 ; Vol. 13, No. 1.
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