Control of mammalian translation by mRNA structure near caps
Open accessAbstract
The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5′ methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5′-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from −10 to −50 kcal/mol and 5′ G cap-to-hairpin distances of 1–46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ΔG = −25 to −35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5′ cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5′-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5′ UTRs.
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Sequences of human or rabbit α- and β-globin or of rabbit β-globin have been used to improve translational efficiency of heterologous mRNAs.
“In particular, sequences of human or rabbit α- and β-globin or of rabbit β-globin have been used to improve translational efficiency of heterologous mRNAs [36,37,38].”
From Effects of Combinations of Untranslated-Region Sequences on Translation of mRNA (2023) · cites this paper as [36]
The ‘Translation efficiency with natural 5′ UTRs’ section reports cloning α- and β-globin 5′ UTRs into a GFP reporter and finding greater translation efficiency than with the designed hairpin set. This supports the use of globin sequences with a heterologous mRNA, but the paper does not identify those globin sequences as human or rabbit or establish every species-specific example in the citing sentence. (LLM, conf=0.84)
Experimental — accuracy not yet measuredGlobin gene sequences are often used to ensure high translation efficiency.
“Globin gene sequences are often used to ensure high translation efficiency.”
From Untranslated Region Sequences and the Efficacy of mRNA Vaccines against Tuberculosis (2024) · cites this paper as [9]
Efficiency of eukaryotic 5′ UTRs depends on length, stability, secondary structure features and positioning, nucleotide composition, and other factors.
“The efficiency of eukaryotic 5′ UTRs depends on their length, stability, secondary structure features and positioning, nucleotide composition, and other factors [20].”
From Identification of novel 5’ UTR variants for enhanced mRNA translation and vaccine immunogenicity (2026) · cites this paper as [20]
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Cites
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“Mammalian 5’ UTRs vary greatly in length and secondary structure with longer, and more structurally stable UTRs correlating with reduced capdependent ribosome scanning and translation efficiency ( (36); reviewed in (21)).”
BackgroundIdentification of novel 5’ UTR variants for enhanced mRNA translation and vaccine immunogenicity
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- Authors
- Babendure, J. R., Babendure, J. L., Ding, J.-H., & Tsien, R. Y.
- Affiliations
- University of California San Diego (US)
- Howard Hughes Medical Institute (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-03-15
- Volume
- 12
- Issue
- 5
- Pages
- 851-861
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC1440912
- OpenAlex
- W2152052780
- Cited by
- 339
- References
- 2
- Citations by year
- 2026: 23 · 2025: 21 · 2024: 21 · 2023: 25 · 2022: 37 · 2021: 33 · 2020: 15 · 2019: 19 · 2018: 24 · 2017: 22 · 2016: 16 · 2015: 13 · 2014: 10 · 2013: 10 · 2012: 12
- FWCI
- 2.27
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Education
- Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- National Institutes of Health
- U.S. Public Health Service (27177)
- National Institute of General Medical Sciences (GM72033, P20GM072033)
- National Institute of Neurological Disorders and Stroke (R37NS027177, R01NS027177)
- 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
- mRNA secondary structure, translation efficiency, 5' untranslated region, 5' cap, hairpin stability, GC content, live-cell imaging
- MeSH terms
- Tripartite Motif Proteins, Animals, Base Sequence, Carrier Proteins, Cells, Cultured, Chlorocebus aethiops, Cytomegalovirus, DNA-Binding Proteins, Fibroblasts, Cricetinae, Molecular Sequence Data, Nuclear Proteins, Promoter Regions, Genetic, RNA Caps, RNA, Viral, CHO Cells, COS Cells, Ubiquitin-Protein Ligases, DNA Repair Enzymes, Mice, Fibroblast Growth Factor 5, In Vitro Techniques
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