Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

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Ivanov, Ivaylo P.
Firth, Andrew E.
Michel, Audrey M.
Atkins, John F.
Baranov, Pavel V.
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Oxford University Press
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In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized-both for increased coding capacity and potentially also for novel regulatory mechanisms-remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.
Eukaryotic translation initiation , Hydroquinone NADH oxidase , Transfer RNA synthetases , Start codon recognition , Messenger RNAs , Saccharomyces-cerevisiae , Phylogenetic analysis , Maximum likelihood , Growth-factor , Gene encodes
Ivanov, I. P., Firth, A. E., Michel, A. M., Atkins, J. F. and Baranov, P. V. (2011) 'Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences', Nucleic Acids Research, 39(10), pp. 4220-4234. doi: 10.1093/nar/gkr007