ArticleRNA (New York, N.Y.)2019
Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 43 citations in OpenAlex.
- Ribosome stalling position, spacing, and A-site occupancy impact translation and cotranslational mRNA decay in plants.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Overlapping upstream ORFs repress translation and expand proteome diversity in Arabidopsis.bioRxiv : the preprint server for biology · 2026Article
- Computational prediction-combined proteogenomics unveils widespread non-AUG translation initiation events in plants.Nucleic acids research · 2026Article
- TISCalling: leveraging machine learning to identify translational initiation sites in plants and viruses.Plant molecular biology · 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
- Modeling alternative translation initiation sites in plants reveals evolutionarily conservedGenome research · 2024Article
- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation.Plant, cell & environment · 2022Article
- Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize.Plant physiology · 2021Article
- Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco.The Plant cell · 2021Article
- Determinants of genome-wide distribution and evolution of uORFs in eukaryotes.Nature communications · 2021Article
- Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants.Frontiers in plant science · 2021Review
- Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation.Annual review of genetics · 2020Review
- Translational gene regulation in plants: A green new deal.Wiley interdisciplinary reviews. RNA · 2020Review
- Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.Scientific reports · 2020Article
- Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants.Genome research · 2020Article
- uORF Shuffling Fine-Tunes Gene Expression at a Deep Level of the Process.Plants (Basel, Switzerland) · 2020Review
- Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel
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Registered trials
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.