Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

• DOI: 10.7554/elife.03528
• Publication Date: 2014-08-21T11:38:16Z
• Authors: Julie L Aspden; Ying Chen Eyre-Wa...; Rose J Phillips; Unum Amin; Muhammad Ali S Mu...; Michele Brocard; Juan-Pablo Couso
• Keywords: 0301 basic medicine; transmembrane peptide; RNA, Untranslated; small open reading Frame; QH301-705.5; Science; non-coding RNA; Biochemistry; Cell Line; Open Reading Frames; 03 medical and health sciences; Animals; Drosophila Proteins; RNA, Messenger; Biology (General); 3' Untranslated Regions; Genome; Q; R; Computational Biology; High-Throughput Nucleotide Sequencing; Reproducibility of Results; Molecular Weight; Drosophila melanogaster; Polyribosomes; Protein Biosynthesis; Medicine; Peptides; Ribosomes

Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear. In this study, we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions in Drosophila. We detect two types of smORFs bound by multiple ribosomes and thus undergoing productive translation. The ‘longer’ smORFs of around 80 amino acids resemble canonical proteins in translational metrics and conservation, and display a propensity to contain transmembrane motifs. The ‘dwarf’ smORFs are in general shorter (around 20 amino-acid long), are mostly found in 5′-UTRs and non-coding RNAs, are less well conserved, and have no bioinformatic indicators of peptide function. Our findings indicate that thousands of smORFs are translated in metazoan genomes, reinforcing the idea that smORFs are an abundant and fundamental genome component.