Date of Award

Spring 1-1-2015

Document Type


Degree Name

Doctor of Philosophy (PhD)

First Advisor

Robin D. Dowell

Second Advisor

Mark Winey

Third Advisor

Rui Yi

Fourth Advisor

Norm Pace

Fifth Advisor

Roy Parker


Most genetic variants associated with disease occur within regulatory regions of the genome, underscoring the need to define the mechanisms that control differences in gene expression regulation between individuals. I discovered a pair of co-regulated, divergently oriented transcripts, AQY2 and ncFRE6, that are expressed in one strain of S.cerevisiae, ∑1278b, but not in another, S288c. By combining classical genetics techniques with high-throughput sequencing, I identified a trans-acting single nucleotide polymorphism within the transcr¬iption factor RIM101 that causes the background-dependent expression of both transcripts. Subsequent RNA-seq experiments revealed that deletion of RIM101 in both backgrounds abrogated the majority of differential expression between S288c and ∑1278b and showed that RIM101 regulates many more targets in S288c than in ∑1278b. However, expression profiling of both strains harboring either RIM101 allele revealed that only three transcripts undergo a significant allele-dependent change in expression. Strikingly, hundreds of RIM101-dependent targets underwent a subtle but consistent shift in expression in the S288c RIM101-swapped strain, but not its ∑1278b counterpart. I conclude that ∑1278b may harbor a variant(s) that buffers against widespread transcriptional dysregulation upon introduction of a non-native RIM101 allele, emphasizing the importance of accounting for genetic background when assessing the impact of a regulatory variant.