ArticleGenome biology2020
Developmental regulation of canonical and small ORF translation from mRNAs.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 51 citations in OpenAlex.
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- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
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- Micropeptide SCAPEP triggers lung adenocarcinoma tumorigenesis via regulating autophagy by promoting CDK15-mediated phosphorylation of vimentin.Cell death & disease · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- Analysis of stress-induced small proteins inScience signaling · 2025Article
- Analysis of stress-induced small proteins inbioRxiv : the preprint server for biology · 2025Article
- Translational activity of 80S monosomes varies dramatically across different tissues.Nucleic acids research · 2025Article
- Pervasiveness of Microprotein Function AmongstCells · 2024Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- Small ORFs, Big Insights:Cells · 2024Review
- Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.Nature cardiovascular research · 2024Article
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
- Micropeptides: origins, identification, and potential role in metabolism-related diseases.Journal of Zhejiang University. Science. B · 2023Review
- Molecular and functional characterization of the Drosophila melanogaster conserved smORFome.Cell reports · 2023Article
- Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer.International journal of molecular sciences · 2023Review
- The rich non-coding RNA landscape of the Drosophila antenna.Cell reports · 2023Article
- The translational landscape of bread wheat during grain development.The Plant cell · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundRibosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis.
resultsWe obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition.
conclusionsWe suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
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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.