The evolution and function of regulatory regions in yeast

Abstract

Gene regulatory changes have long been theorized to be a source of evolutionary novelty. In more recent years, we have learned that noncoding changes can have a large effect on phenotype and disease and can be of evolutionary importance in a variety of model systems. However, the study of regulatory regions is still hampered by challenges in identifying functional noncoding regions and testing their effects, and as such many basic questions remain unanswered about these regions. Namely, what is the location of functional regulatory regions, how does evolution affect these regulatory regions, what is their effect if altered on downstream traits such as gene expression, and what are the best ways to test these effects? In this dissertation, I use yeast as a model organism to assess the effects of noncoding variants and chromatin architecture on gene expression. I first address the question of how best to test for effects of genetic mutations on phenotypes by asking how well association mapping works in yeast and find that population structure complicates the use of yeast in association mapping without careful choice of which strains to use. Secondly, I assess the evolutionary pressures acting on noncoding regions in yeast, specifically the differences in pressures on potentially functional sites, motif binding sites, and the other noncoding sites, and find that there is strong purifying pressure acting at motif binding sites. I then use data from yeast strains to associate noncoding variants with differences in gene expression. Finally, I use methods to map chromatin accessibility to ask how differences in accessibility of open chromatin regions upstream of genes affect differences in gene expression between species. I find that differences in chromatin accessibility are numerous, that these differences appear to be driven primarily by genetic changes in cis, and that the effects of chromatin accessibility on gene expression are modest. In conclusion, my thesis work has mapped regulatory regions in yeast, revealed the functional effects of these regions and the variants that lie within them, and suggested alternative methods for associating genetic variation with phenotypes in yeast.