Functional and non-functional classes of peptides produced bylong non-coding RNAs

Cells express thousands of transcripts that show weak coding potential. Known as long non-coding RNAs (lncRNAs), they typically contain short open reading frames (ORFs) having no homology with known proteins. Recent studies have reported that a significant proportion of lncRNAs are translated, challenging the view that they are essentially non-coding. These results are based on the selective sequencing of ribosome-protected fragments, or ribosome profiling. The present study used ribosome profiling data from eight mouse tissues and cell types, combined with ~330,000 synonymous and non-synonymous single nucleotide variants, to dissect the biological implications of lncRNA translation. Using the three-nucleotide read periodicity that characterizes actively translated regions, we found that about 23% of the transcribed lncRNAs was translated (1,365 out of 6,390). About one fourth of the translated sequences (350 lncRNAs) showed conservation in humans; this is likely to produce functional micropeptides, including the recently discovered myoregulin. For other lncRNAs, the ORF codon usage bias distinguishes between two classes. The first has significant coding scores and contains functional proteins which are not conserved in humans. The second large class, comprising >500 lncRNAs, produces proteins that show no significant purifying selection signatures. We showed that the neutral translation of these lncRNAs depends on the transcript expression level and the chance occurrence of ORFs with a favorable codon composition. This provides the first evidence to data that many lncRNAs produce non-functional proteins.