Date of Award

Summer 8-15-2015

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Understanding how cis-regulatory regions function and evolve has been a long-standing challenge. To address this issue, I take two approaches: an experimental approach to understand yeast MLS1 promoter evolution and a theoretical approach to understand how harmful mutations may interact. With respect to my experimental approach, previous studies have shown that in many cases orthologous cis-regulatory regions from divergent species have conserved patterns of gene activation and repression when placed into the same genetic background. While these studies are informative, in order to understand if diverged cis-regulatory sequences are truly functionally equivalent, it is vital that the fitness consequences of diverged promoters are measured in addition to gene expression. To address this, I investigated whether highly diverged promoters for the gene malate synthase (MLS1) from diverged yeast species are able to rescue both gene expression levels as well as fitness when these diverged promoters are placed into S. cerevisiae upstream of the S. cerevisiae MLS1 gene. These experiments indicate that promoters with high sequence divergence do activate expression of MLS1 in S. cerevisiae, but often to lower levels than the S. cerevisiae MLS1 promoter. Interestingly, lower expression levels did not translate into lower growth rates except in the case of one promoter with the weakest activation. Additionally, I generated single base pair deletions within a transcription factor binding site of the MLS1 promoter and found that none of the deletions had a detectable impact on fitness. These findings indicate that expression changes that result from cis-regulatory evolution do not always translate into significant changes in fitness. Moreover, these results suggest that there is epistasis among harmful mutations in a cis-regulatory region. Therefore, to address the fitness consequences of epistatic interactions among harmful mutations in a population, I took a theoretical approach and developed a model of additive fitness effects. I demonstrated that this model increases the predicted average fitness in a population compared to the fitness predicted under a model of independent, multiplicative effects. I also demonstrated that this model is consistent with mutation accumulation data. Together, these experimental and theoretical studies help elucidate how cis-regulatory regions evolve and function and also provide a theoretical framework for how harmful mutations, including regulatory mutations, may impact populations over evolutionary time.


English (en)

Chair and Committee

Justin C Fay

Committee Members

Barak A Cohen, Joseph C Corbo, Allan Larson, Heather L True-Krob,


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Available for download on Thursday, August 15, 2115

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