Identification of expressed and conserved human noncoding RNAs
- Morten Muhlig Nielsen1,4,
- Disa Tehler2,
- Søren Vang1,
- Frantisek Sudzina1,3,
- Jakob Hedegaard1,
- Iver Nordentoft1,
- Torben Falck Ørntoft1,
- Anders H. Lund2 and
- Jakob Skou Pedersen1,4
- 1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
- 2Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
Abstract
The past decade has shown mammalian genomes to be pervasively transcribed and identified thousands of noncoding (nc) transcripts. It is currently unclear to what extent these transcripts are of functional importance, as experimental functional evidence exists for only a small fraction. Here, we characterize the expression and evolutionary conservation properties of 12,115 known and novel nc transcripts, including structural RNAs, long nc RNAs (lncRNAs), antisense RNAs, EvoFold predictions, ultraconserved elements, and expressed nc regions. Expression levels are evaluated across 12 human tissues using a custom-designed microarray, supplemented with RNAseq. Conservation levels are evaluated at both the base level and at the syntenic level. We combine these measures with epigenetic mark annotations to identify subsets of novel nc transcripts that show characteristics similar to known functional ncRNAs. Few novel nc transcripts show both high expression and conservation levels. However, overall, we observe a positive correlation between expression and both conservation and epigenetic annotations, suggesting that a subset of the expressed transcripts are under purifying selection and likely functional. The identified subsets of expressed and conserved novel nc transcripts may form the basis for further functional characterization.
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↵4 Corresponding authors
E-mail morten.muhlig{at}ki.au.dk
E-mail jakob.skou{at}ki.au.dk
- Received March 2, 2013.
- Accepted November 7, 2013.
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