The Emerging World of Small ORFs

Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found in plant viral RNAs and considered an interesting curiosity, an increasing number of these sORFs have been shown to encode functional peptides or play a regulatory role. The recent discovery that many of these sORFs initiate with start codons other than AUG, together with the identification of functional small peptides encoded in supposedly noncoding primary miRNA transcripts (pri-miRs), has drastically increased the number of potentially functional sORFs within the genome. Here we review how advances in technology, notably ribosome profiling (RP) assays, are complementing bioinformatics and proteogenomic methods to provide powerful ways to identify these elusive features of plant genomes, and highlight the regulatory roles sORFs can play. Small open reading frames (sORFs) that encode peptides that are 100 amino acids or fewer in length are underrepresented in genome annotations. Ribosome profiling techniques, along with protein mass spectrometry and new bioinformatics approaches, are being used to support annotation of these features. sORFs have been found in coding and noncoding RNA. In plants and animals, several sORFs have been shown to initiate with non-AUG start codons.