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

• Published in: eLife Vol. 3; p. e03528
• Main Authors: Aspden, Julie L, Eyre-Walker, Ying Chen, Phillips, Rose J, Amin, Unum, Mumtaz, Muhammad Ali S, Brocard, Michele, Couso, Juan-Pablo
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 21.08.2014; eLife Sciences Publications, Ltd
• Subjects: 3' Untranslated Regions - genetics; Amino acids; Animals; Annotations; Biochemistry; Cell Line; Computational Biology - methods; Drosophila; Drosophila melanogaster - cytology; Drosophila melanogaster - genetics; Drosophila Proteins - chemistry; Drosophila Proteins - genetics; Experiments; Footprints; Genes; Genome - genetics; Genomes; Genomics and Evolutionary Biology; High-Throughput Nucleotide Sequencing - methods; Insects; Mass spectrometry; Molecular Weight; non-coding RNA; Open reading frames; Open Reading Frames - genetics; Peptides; Peptides - chemistry; Peptides - genetics; Polyribosomes - genetics; Polyribosomes - metabolism; Protein Biosynthesis; Proteins; Reproducibility of Results; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Untranslated - genetics; Scientific imaging; small open reading Frame; Translation; transmembrane peptide; d. melanogaster; evolutionary biology; non-coding RNAs; biochemistry; small open reading Frames; genomics; transmembrane peptides
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.03528

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.