PT - JOURNAL ARTICLE AU - Hiro Takahashi AU - Shido Miyaki AU - Hitoshi Onouchi AU - Taichiro Motomura AU - Nobuo Idesako AU - Anna Takahashi AU - Shuichi Fukuyoshi AU - Toshinori Endo AU - Kenji Satou AU - Satoshi Naito AU - Motoyuki Itoh TI - Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes AID - 10.1101/672840 DP - 2019 Jan 01 TA - bioRxiv PG - 672840 4099 - http://biorxiv.org/content/early/2019/06/17/672840.short 4100 - http://biorxiv.org/content/early/2019/06/17/672840.full AB - Background Upstream open reading frames (uORFs) are located in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded in these regions play important regulatory roles in controlling main ORF (mORF) translation. To comprehensively identify uORFs encoding functional peptides, genome-wide searches for uORFs with conserved peptide sequences (CPuORFs) have been conducted in various organisms using comparative genomic approaches. However, in animals, CPuORFs have been identified only by comparing uORF sequences between a limited number of closely related species, and it is unclear how many previously identified CPuORFs encode regulatory peptides.Results Here, we conducted exhaustive genome-wide searches for animal CPuORFs conserved in various taxonomic ranges, using the ESUCA pipeline, which we recently developed for efficient comprehensive identification of CPuORFs. ESUCA can efficiently compare uORF sequences between an unlimited number of species using BLAST and automatically determine the taxonomic ranges of sequence conservation for each CPuORF. By applying ESUCA to human, chicken, zebrafish, and fruit fly genomes, 1,430 (1,339 novel and 91 known) CPuORFs were identified. We examined the effects of 14 human CPuORFs on mORF translation using a transient expression assay. Through this analysis, we identified six novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, all of which were conserved beyond Amniota.Conclusions We discovered a much higher number of animal CPuORFs than previously identified. Furthermore, our results suggest that human CPuORFs conserved beyond Amniota are more likely to encode regulatory peptides than those conserved in narrower taxonomic ranges.