GC content shapes mRNA storage and decay in human cells
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Abstract
mRNA translation and decay appear often intimately linked although the rules of this interplay are poorly understood. In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors, and with available CLIP and related data. This revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA stability: P-bodies contain mostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich and GC-rich transcripts tend to follow distinct decay pathways; and the targets of sequence-specific RBPs and miRNAs are also biased in terms of GC content. Altogether, these results suggest an integrated view of post-transcriptional control in human cells where most translation regulation is dedicated to inefficiently translated AU-rich mRNAs, whereas control at the level of 5’ decay applies to optimally translated GC-rich mRNAs.
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GC-rich mRNAs tend to be more stable than AU-rich mRNAs.
“First, GC-rich mRNAs tend to be more stable than AU-rich mRNAs [32].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [32]
The Results (Figure 4) report that silencing XRN1 stabilizes GC-rich mRNAs, while silencing PAT1B stabilizes AU-rich mRNAs. The Discussion describes distinct decay and storage pathways, but neither passage compares the groups’ overall stability. Searches for relative stability and half-life found no such comparison in our copy. (LLM, conf=0.74)
Experimental — accuracy not yet measuredOptimization of mRNA secondary structure and stability can be achieved by increasing the GC content of the coding sequence.
“Optimization of mRNA secondary structure244,245 and stability can be achieved by increasing the GC content of the coding sequence.246–248”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [247]
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Huang, E., Fu, T., Zhang, L., Yan, G., Yamamoto, R., Terrazas, S., Nguyen, T. L., Gonzalez‐Figueroa, C., Khanbabaei, A., Bahn, J. H., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02326-8 · Cited by 9 · see citing works
- Authors
- Courel, M., Clément, Y., Bossevain, C., Foretek, D., Vidal Cruchez, O., Yi, Z., Bénard, M., Benassy, M.-N., Kress, M., Vindry, C., Ernoult-Lange, M., Antoniewski, C., Morillon, A., Brest, P., Hubstenberger, A., Roest Crollius, H., Standart, N., & Weil, D.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- École Normale Supérieure - PSL (FR)
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Nice, France
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
- University of Cambridge (GB)
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2019-12-19
- Volume
- 8
- Pages
- e49708
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC6944446
- OpenAlex
- W2994774550
- Cited by
- 250
- References
- 83
- Citations by year
- 2026: 38 · 2025: 40 · 2024: 44 · 2023: 35 · 2022: 25 · 2021: 44 · 2020: 17 · 2019: 7
- FWCI
- 7.98
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Association pour la Recherche sur le Cancer (Subvention Fixe)
- Agence Nationale de la Recherche (ANR-14-CE09-0013-01, ANR-11-LABX-0028-01)
- European Research Council (DARK consolidator grant)
- Canceropôle PACA
- Biotechnology and Biological Sciences Research Council
- Isaac Newton Trust
- Fondation Philippe Wiener - Maurice Anspach
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- GC content, mRNA stability, mRNA degradation, P-bodies, codon usage, translational regulation, post-transcriptional regulation, RNA-binding proteins, microRNA, human cells
- MeSH terms
- Base Composition, Gene Expression Regulation, Humans, RNA, Messenger, Protein Biosynthesis, RNA Stability, RNA, Messenger, Stored, MicroRNAs, Transcriptome
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