ArticleBMC genomics2020
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 19 citations in OpenAlex.
- Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering.The Plant journal : for cell and molecular biology · 2025Review
- Plant engineering: advances, bottlenecks, and promise.The Plant journal : for cell and molecular biology · 2025Article
- A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism.Nature communications · 2025Article
- Discovery of a conserved translationally repressive upstream open reading frame within the iron-deficiency response regulator IDEF2.BMC plant biology · 2024Article
- What, where, and how: Regulation of translation and the translational landscape in plants.The Plant cell · 2024Review
- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- Principles, mechanisms, and biological implications of translation termination-reinitiation.RNA (New York, N.Y.) · 2023Article
- Upstream open reading frame-mediated upregulation of ANAC082 expression in response to nucleolar stress in Arabidopsis.Plant biotechnology (Tokyo, Japan) · 2023Article
- Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation.Plant, cell & environment · 2022Article
- The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.The Plant cell · 2021Article
- Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation.Annual review of genetics · 2020Review
- Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.Scientific reports · 2020Article
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundUpstream open reading frames (uORFs) in the 5'-untranslated regions (5'-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.
resultsTo efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.
conclusionsThis study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.