Upstream ORFs are prevalent translational repressors in vertebrates
Open accessAbstract
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii)uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.
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Sequences with out-of-frame upstream start codons (uAUGs) or upstream open reading frames (uORFs) show decreased ribosome loading.
“Our data clearly show the expected decrease in ribosome loading for sequences with either out-of-frame upstream start codons (uAUGs) (Fig. 1c) or upstream open reading frames (uORFs) (Supplementary Fig. 2b)18,19.”
From Human 5′ UTR design and variant effect prediction from a massively parallel translation assay (2019) · cites this paper as [19]
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Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
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“However, it remains unclear what proportion of these are regulatory ORFs that do not produce functional peptides and instead compete with the canonical CDS for ribosome binding, or else are simply stochastic interactions (Calvo et al. 2009; Bazzini et al. 2014; Johnstone et al. 2016).”
Background
- Authors
- Johnstone, T. G., Bazzini, A. A., & Giraldez, A. J.
- Affiliations
- Yale University (US)
- Venue
- The EMBO Journal
- Published
- 2016-02-19
- Volume
- 35
- Issue
- 7
- Pages
- 706-723
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC4818764
- OpenAlex
- W2282922301
- Cited by
- 346
- References
- 8
- Citations by year
- 2026: 29 · 2025: 32 · 2024: 41 · 2023: 38 · 2022: 29 · 2021: 43 · 2020: 45 · 2019: 29 · 2018: 28 · 2017: 21 · 2016: 11
- FWCI
- 12.67
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of Health (T32GM007499, R01GM081602‐07, R01GM103789‐03, R01HD074078‐03)
- Pew Fellows Program in Biomedical Sciences
- Pew Scholars Program in the Biomedical Sciences
- March of Dimes
- Yale Scholars Program
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- upstream open reading frames, protein synthesis inhibition, 5' untranslated region, post-transcriptional regulation, ribosome profiling, mRNA leader sequence
- MeSH terms
- Animals, Repressor Proteins, Transcription, Genetic, Protein Biosynthesis, Vertebrates, Open Reading Frames
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