  Deep transcriptome sequencing has revealed the existence of many transcripts
that lack long or conserved open reading frames and which have been termed long
non-coding RNAs (lncRNAs). Despite the existence of several well-characterized
lncRNAs that play roles in the regulation of gene expression, the vast majority
of them do not yet have a known function. Motivated by the existence of
ribosome profiling data for several species, we have tested the hypothesis that
they may act as a repository for the synthesis of new peptides using data from
human, mouse, zebrafish, fruit fly, Arabidopsis and yeast. The ribosome
protection patterns are consistent with the presence of translated open reading
frames (ORFs) in a very large number of lncRNAs. Most of the ribosome-protected
ORFs are shorter than 100 amino acids and usually cover less than half the
transcript. Ribosome density in these ORFs is high and contrasts sharply with
the 3UTR region, in which very often there is no detectable ribosome binding,
similar to bona fide protein-coding genes. The coding potential of
ribosome-protected ORFs, measured using hexamer frequencies, is significantly
higher than that of randomly selected intronic ORFs and similar to that of
evolutionary young coding sequences. Selective constraints in
ribosome-protected ORFs from lncRNAs are lower than in typical protein-coding
genes but again similar to young proteins. These results strongly suggest that
lncRNAs play an important role in de novo protein evolution.
