Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
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Abstract
Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein coexpression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype–phenotype relationship.
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Correlation between the mRNAs for the paired RNA-Seq relative to the global proteomics datasets showed lower positive Pearson correlation values ranging from 0.333 - 0.378 for all genotypes tested.
“Correlation between the mRNAs for the paired RNA-Seq relative to the global proteomics datasets showed lower positive Pearson correlation values ranging from 0.333 – 0.378 for all genotypes tested which is consistent with prior studies on transcriptome / proteome correlation82–84.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [82]
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Self-citationSayols, S. (2020) · NCI BioConductor · doi:10.18129/b9.bioc.rrvgo · Cited by 6 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- [85]E. M. Teyssonniere, Raw data for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast. PRIDE. http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD044523. Deposited 12 August 2023. PMC11087752 38696467
- [86]E. M. Teyssonniere, Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast. Zenodo. 10.5281/zenodo.10567083. Deposited 24 January 2024. PMC11087752 38696467 · DOI
- [87]E. M. Teyssonniere, Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast. GitHub. https://github.com/HaploTeam/eQTL_pQTL. Deposited 25 January 2024. PMC11087752 38696467
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- Authors
- Teyssonnière, E. M., Trébulle, P., Muenzner, J., Loegler, V., Ludwig, D., Amari, F., Mülleder, M., Friedrich, A., Hou, J., Ralser, M., & Schacherer, J.
- Affiliations
- UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Université de Strasbourg, CNRS, Strasbourg 67000, France
- Centre for Human Genetics (GB)
- Charité – Universitätsmedizin Berlin (DE)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Trébulle, Pauline
- Muenzner, Julia
- Ralser, Markus
- Schacherer, Joseph
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2024-05-02
- Volume
- 121
- Issue
- 19
- Pages
- e2319211121-e2319211121
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC11087752
- OpenAlex
- W4396596344
- Cited by
- 40
- References
- 87
- Citations by year
- 2026: 17 · 2025: 16 · 2024: 7
- FWCI
- 5.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- HAL (submittedVersion, cc-by-nc-nd)
- Funders
- HHS | National Institutes of Health (R01 (GM147040-01))
- EC | ERC | HORIZON EUROPE European Research Council (ERC Consolidator grant (772505), ERC Synergy grant)
- Wellcome Trust (Wellcome Trust Grant)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- gene expression variation, Saccharomyces cerevisiae, quantitative proteomics, transcriptome, protein abundance, mRNA-protein correlation, expression quantitative trait loci, protein quantitative trait loci, genotype-phenotype correlation, protein turnover, natural yeast isolates
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