Long non-coding RNAs as a source of new peptides

Elife. 2014 Sep 16;3:e03523. doi: 10.7554/eLife.03523.

Abstract

Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.

Keywords: de novo gene evolution; eukaryote; evolutionary biology; genomics; human; lncRNA; ribosome profiling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis
  • Drosophila melanogaster
  • Evolution, Molecular
  • Gene Expression Profiling
  • Humans
  • Mice
  • Open Reading Frames / genetics*
  • Peptides / genetics*
  • Protein Biosynthesis*
  • Proteomics
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Saccharomyces cerevisiae
  • Selection, Genetic
  • Sequence Analysis, RNA
  • Species Specificity
  • Zebrafish

Substances

  • Peptides
  • RNA, Long Noncoding

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.