Details
| Original language | English |
|---|---|
| Article number | 20240582 |
| Journal | Journal of the Royal Society Interface |
| Volume | 22 |
| Issue number | 224 |
| Publication status | Published - 19 Mar 2025 |
Abstract
Extensive efforts have been devoted to enhancing the translation efficiency of mRNA delivered to mammalian cells via codon optimization. However, the impact of codon choice on mRNA stability remains underexplored. In this study, we investigated the influence of codon usage on mRNA degradation kinetics in cultured human cell lines using live-cell imaging on single-cell arrays. By measuring mRNA lifetimes at the single-cell level for synthetic mRNA constructs, we confirmed that mRNAs containing slowly translated codon windows have shorter lifetimes. Unexpectedly, these mRNAs did not exhibit decreased stability in the presence of small interfering RNA (siRNA) compared with the unmutated sequence, suggesting an interference of different concurrent degradation mechanisms. We employed stochastic simulations to predict ribosome density along the open reading frame, revealing that the ribosome densities correlated with mRNA stability in a cell-type- and codon-position-specific manner. In summary, our results suggest that the effect of codon choice and its influence on mRNA lifetime is context-dependent with respect to cell type, codon position and RNA interference.
Keywords
- mRNA, mRNA stability, RNA interference, single-cell, slow-codon windows
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biotechnology
- Biochemistry, Genetics and Molecular Biology(all)
- Biophysics
- Chemical Engineering(all)
- Bioengineering
- Materials Science(all)
- Biomaterials
- Biochemistry, Genetics and Molecular Biology(all)
- Biochemistry
- Engineering(all)
- Biomedical Engineering
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In: Journal of the Royal Society Interface, Vol. 22, No. 224, 20240582, 19.03.2025.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Less is more
T2 - slow-codon windows enhance eGFP mRNA resilience against RNA interference
AU - Müller, Judith A.
AU - Schwake, Gerlinde
AU - Reiser, Anita
AU - Woschée, Daniel
AU - Alirezaeizanjani, Zahra
AU - Rädler, Joachim O.
AU - Rudorf, Sophia
N1 - Publisher Copyright: © 2025 The Author(s).
PY - 2025/3/19
Y1 - 2025/3/19
N2 - Extensive efforts have been devoted to enhancing the translation efficiency of mRNA delivered to mammalian cells via codon optimization. However, the impact of codon choice on mRNA stability remains underexplored. In this study, we investigated the influence of codon usage on mRNA degradation kinetics in cultured human cell lines using live-cell imaging on single-cell arrays. By measuring mRNA lifetimes at the single-cell level for synthetic mRNA constructs, we confirmed that mRNAs containing slowly translated codon windows have shorter lifetimes. Unexpectedly, these mRNAs did not exhibit decreased stability in the presence of small interfering RNA (siRNA) compared with the unmutated sequence, suggesting an interference of different concurrent degradation mechanisms. We employed stochastic simulations to predict ribosome density along the open reading frame, revealing that the ribosome densities correlated with mRNA stability in a cell-type- and codon-position-specific manner. In summary, our results suggest that the effect of codon choice and its influence on mRNA lifetime is context-dependent with respect to cell type, codon position and RNA interference.
AB - Extensive efforts have been devoted to enhancing the translation efficiency of mRNA delivered to mammalian cells via codon optimization. However, the impact of codon choice on mRNA stability remains underexplored. In this study, we investigated the influence of codon usage on mRNA degradation kinetics in cultured human cell lines using live-cell imaging on single-cell arrays. By measuring mRNA lifetimes at the single-cell level for synthetic mRNA constructs, we confirmed that mRNAs containing slowly translated codon windows have shorter lifetimes. Unexpectedly, these mRNAs did not exhibit decreased stability in the presence of small interfering RNA (siRNA) compared with the unmutated sequence, suggesting an interference of different concurrent degradation mechanisms. We employed stochastic simulations to predict ribosome density along the open reading frame, revealing that the ribosome densities correlated with mRNA stability in a cell-type- and codon-position-specific manner. In summary, our results suggest that the effect of codon choice and its influence on mRNA lifetime is context-dependent with respect to cell type, codon position and RNA interference.
KW - mRNA
KW - mRNA stability
KW - RNA interference
KW - single-cell
KW - slow-codon windows
UR - http://www.scopus.com/inward/record.url?scp=105000423193&partnerID=8YFLogxK
U2 - 10.1098/rsif.2024.0582
DO - 10.1098/rsif.2024.0582
M3 - Article
AN - SCOPUS:105000423193
VL - 22
JO - Journal of the Royal Society Interface
JF - Journal of the Royal Society Interface
SN - 1742-5689
IS - 224
M1 - 20240582
ER -