ArticlePLoS biology2018
Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.
Article in PLoS biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Regulatory landscape of widespread stop codon readthrough inbioRxiv : the preprint server for biology · 2026Article
- The birth, death, and evolutionary compensation of uORFs in Drosophila.Nucleic acids research · 2026Article
- Flexibility and modulation of translation initiation in enterovirus genomes.PLoS pathogens · 2026Article
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering.Annual review of phytopathology · 2025Review
- Article
- Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythms and sleep.PLoS biology · 2025Article
- Integrative multi-omics analysis reveals the translational landscape of the plant-parasitic nematode Meloidogyne incognita.Communications biology · 2025Article
- Tiny but mighty: Diverse functions of uORFs that regulate gene expression.Computational and structural biotechnology journal · 2024Review
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Upstream open reading frames repress the translation from the iab-8 RNA.PLoS genetics · 2024Article
- The molecular basis of phenotypic evolution: beyond the usual suspects.Trends in genetics : TIG · 2024Review
- Article
- Application of genome editing techniques to regulate gene expression in crops.BMC plant biology · 2024Review
- An epitope encoded by uORF ofMolecular therapy oncolytics · 2023Article
- Tuning plant phenotypes by precise, graded downregulation of gene expression.Nature biotechnology · 2023Article
- Article
- Article
- Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues.Genome biology · 2023Article
- Translational regulation by uORFs and start codon selection stringency.Genes & development · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Upstream open reading frames (uORFs) play important roles in regulating the main coding DNA sequences (CDSs) via translational repression. Despite their prevalence in the genomes, uORFs are overall discriminated against by natural selection. However, it remains unclear why in the genomes there are so many uORFs more conserved than expected under the assumption of neutral evolution. Here, we generated genome-wide maps of translational efficiency (TE) at the codon level throughout the life cycle of Drosophila melanogaster. We identified 35,735 uORFs that were expressed, and 32,224 (90.2%) of them showed evidence of ribosome occupancy during Drosophila development. The ribosome occupancy of uORFs is determined by genomic features, such as optimized sequence contexts around their start codons, a shorter distance to CDSs, and higher coding potentials. Our population genomic analysis suggests the segregating mutations that create or disrupt uORFs are overall deleterious in D. melanogaster. However, we found for the first time that many (68.3% of) newly fixed uORFs that are associated with ribosomes in D. melanogaster are driven by positive Darwinian selection. Our findings also suggest that uORFs play a vital role in controlling the translational program in Drosophila. Moreover, we found that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner, suggesting that selective transcription or translation of uORFs could potentially modulate the TE of the downstream CDSs during Drosophila development.
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