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Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

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Ralser,  Markus       
Biochemistry and Systems Biology of Metabolism (Markus Ralser), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Teyssonnière, E. M., Trébulle, P., Muenzner, J., Loegler, V., Ludwig, D., Amari, F., et al. (2024). Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast. Proceedings of the National Academy of Sciences of the United States of America, 121(19): Article e2319211121. doi:10.1073/pnas.2319211121.


Cite as: https://hdl.handle.net/21.11116/0000-0010-8F0F-E
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.