ArticleThe Plant cell2024
Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.
Article in The Plant cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 48 citations in OpenAlex.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- FERONIA Modulates Translational Buffering Capacity of Ribosome-Associated Gene Module in Salt-Stressed Tomato Roots.Plants (Basel, Switzerland) · 2026Article
- Overlapping upstream ORFs repress translation and expand proteome diversity in Arabidopsis.bioRxiv : the preprint server for biology · 2026Article
- No Time to Fold: Intrinsically Disordered Microproteins in Action.Biochemistry · 2026Review
- Plant Peptides on the Rise: From Historical Insight to Future Applications.Plant biotechnology journal · 2026Review
- TheGenes · 2026Article
- Plant non-canonical peptides: From identification to mechanisms.Plant communications · 2026Review
- FungiGuard: identification of plant antifungal peptides with artificial intelligence.Genome biology · 2026Article
- Translational landscape during seed germination revealed by ribosome profiling.The Plant journal : for cell and molecular biology · 2026Article
- Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Translational control in plants: from basic mechanisms to environmental and developmental responses.The Plant journal : for cell and molecular biology · 2026Review
- Plant microRNA maturation and function.Nature reviews. Molecular cell biology · 2026Review
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- GC3 codons enhance protein production in diverse GC- and AT-rich plant species.bioRxiv : the preprint server for biology · 2025Article
- Not to be overlooked: dipeptides and their role in plant stress resilience.Journal of experimental botany · 2025Review
- Long Non-Coding RNAs in the Cold-Stress Response of Horticultural Plants: Molecular Mechanisms and Potential Applications.International journal of molecular sciences · 2025Review
- TheGenome research · 2025Article
- Optimised Ribosome Profiling Reveals New Insights Into Translational Regulation in Synchronised Chlamydomonas reinhardtii Cultures.Plant, cell & environment · 2025Article
- TISCalling: leveraging machine learning to identify translational initiation sites in plants and viruses.Plant molecular biology · 2025Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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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 Socratic graph.