title: The Emerging World of Small ORFs.
abstract: 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.
authors.affiliation: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
authors.forename: Roger P
authors.initials: RP
authors.lastname: Hellens
authors.affiliation: Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Brown
authors.affiliation: Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
authors.forename: Matthew A W
authors.initials: MAW
authors.lastname: Chisnall
authors.affiliation: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Waterhouse
authors.affiliation: Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand; New Zealand Institute for Plant and Food Research Ltd. Electronic address: richard.macknight@otago.ac.nz.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Macknight
mesh_terms: D003062:Codon / Q000235:genetics; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D010455:Peptides / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D012270:Ribosomes / Q000235:genetics*
chemical_list: D003062:Codon; D010455:Peptides; D018749:RNA, Plant; D012367:RNA, Viral
keywords: non-AUG translation initiation; ribosome profiling; small open reading frame; translation; upstream open reading frame