Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

Background: The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. Results: We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codon...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Marija Cvijovic, Daniel Dalevi, Elizabeth Bilsland, Graham J. L. Kemp, Per Sunnerhagen
• Keywords: BMCBI 2007, Evolutionary Conservation, Regulatory Role, Spurious UORFs