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Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae

Anastacia N. Wienecke, Margaret L. Barry, View ORCID ProfileDaniel A. Pollard
doi: https://doi.org/10.1101/2022.09.07.507001
Anastacia N. Wienecke
1Biology Department, Western Washington University, 516 High Street, MS9160, Bellingham, WA 98225
2Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Genome Sciences Building, Chapel Hill, NC 27599
3Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Genome Sciences Building, Chapel Hill, NC 27599
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  • For correspondence: wienecke@email.unc.edu pollard@wwu.edu
Margaret L. Barry
1Biology Department, Western Washington University, 516 High Street, MS9160, Bellingham, WA 98225
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Daniel A. Pollard
1Biology Department, Western Washington University, 516 High Street, MS9160, Bellingham, WA 98225
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  • ORCID record for Daniel A. Pollard
  • For correspondence: wienecke@email.unc.edu pollard@wwu.edu
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Abstract

Codon bias and mRNA folding strength (mF) are hypothesized molecular mechanisms by which polymorphisms in genes modify protein expression. Natural patterns of codon bias and mF across genes as well as effects of altering codon bias and mF suggest the influence of these two mechanisms may vary depending on the specific location of polymorphisms within a transcript. Despite the central role codon bias and mF may play in natural trait variation within populations, systematic studies of how polymorphic codon bias and mF relate to protein expression variation are lacking. To address this need, we analyzed genomic, transcriptomic, and proteomic data for 22 Saccharomyces cerevisiae isolates, estimated protein accumulation for each allele of 1620 genes as the log of protein molecules per RNA molecule (logPPR), and built linear mixed effects models associating allelic variation in codon bias and mF with allelic variation in logPPR. We found codon bias and mF interact synergistically in a positive association with logPPR and this interaction explains almost all the effect of codon bias and mF. We examined how the locations of polymorphisms within transcripts influence their effects and found that codon bias primarily acts through polymorphisms in domain encoding and 3’ coding sequences while mF acts most significantly through coding sequences with weaker effects from UTRs. Our results present the most comprehensive characterization to date of how polymorphisms in transcripts influence protein expression.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 09, 2022.
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Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae
Anastacia N. Wienecke, Margaret L. Barry, Daniel A. Pollard
bioRxiv 2022.09.07.507001; doi: https://doi.org/10.1101/2022.09.07.507001
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Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae
Anastacia N. Wienecke, Margaret L. Barry, Daniel A. Pollard
bioRxiv 2022.09.07.507001; doi: https://doi.org/10.1101/2022.09.07.507001

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