Identifying the specific causal DNA differences in a genome that contribute to variation in phenotypic traits is a key goal of genetic research. Trans-acting DNA variants that alter gene expression are important sources of genetic variation. Several genes are known to carry single causal variants that affect the expression of numerous genes in trans. Whether these single variants are representative of the architecture of trans-acting variation is unknown. Here, we studied the gene IRA2, which carries variants with broad, trans-acting effects on gene expression in two strains of the yeast Saccharomyces cerevisiae. We found that IRA2 contains at least seven causal nonsynonymous variants. The causal variants were located throughout the gene body and included a pair of neighboring variants with opposing effects that largely canceled each other out. The causal variants showed evidence for non-additive epistatic interactions, in particular among variants at the 5 end of the gene. These results show that the molecular basis of trans-acting variation can involve considerable complexity even within a single gene.
