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Date of Award

Spring 2025

Document Type

Masters Thesis

Department or Program Affiliation

Biology

Degree Name

Master of Science (MS)

Department

Biology

First Advisor

Pollard, Dan A.

Second Advisor

Lee, Suzanne R.

Third Advisor

Galati, Nick

Abstract

Natural variation in gene expression drives trait differences in organisms, yet the genetic mechanisms underlying this variation remain poorly understood. Polymorphisms in transcript properties such as codon bias, mRNA folding strength, transcription elongation rate, and amino acid properties like charge and weight influence gene expression, with their effects potentially depending on their position within the transcript. Despite their potential role in shaping natural trait variation, systematic studies on how these transcript properties relate to gene expression in Saccharomyces cerevisiae are limited. Our study utilizes genomic, transcriptomic, and proteomic data for 22 S. cerevisiae isolates for 1,447 genes. For each gene, we calculated across-isolate changes for our transcript properties and assessed the impact on mRNA transcript abundance, protein abundance, and translational efficiency using linear mixed-effects models. We found that mRNA folding strength, codon bias, and amino acid (AA) weight had significant effects on all three levels of expression. Codon bias and AA weight have consistent effects across expression levels, however, mRNA folding strength negatively influences transcript abundance while positively influencing translational efficiency and protein abundance. Transcription elongation rate and AA charge have weaker effects and only associate with transcript abundance. Codon bias, AA charge, and AA weight showed synergistic effects with mRNA folding strength, particularly on translational efficiency. The impact of polymorphism location varied: codon bias acted mainly through domain-encoding and 3′ coding regions, while mRNA folding strength effects were concentrated around start/stop codons and within coding regions. Our results provide a comprehensive view of how transcript-level polymorphisms shape gene expression in yeast.

Type

Text

Keywords

natural allelic variation, yeast, protein abundance, mRNA abundance

Publisher

Western Washington University

OCLC Number

1523704909

Subject – LCSH

Messenger RNA; Saccharomyces cerevisiae; Gene expression; Genetic transcription; Genetic polymorphisms

Format

application/pdf

Genre/Form

masters theses

Language

English

Rights

Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.

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