Template Switching as a Driver of Promoter Evolution in Yeast: Case Study of the GRE2 Gene

Inverted repeats (IRs) are sequences with internal symmetry that can form non-canonical DNA structures. DNA polymerase template switching between imperfect IR arms can homogenize the arms and expand their size. IRs play an important role in the binding of transcription factors (TFs), particularly those that function as dimers. We used comparative genomics to identify recent IR-expansions in the vicinity of promoter regions in the lineage of Saccharomyces cerevisiae. From the thousands of events identified, we further focused on ones with significant expansion, outside of simple repeats and within confirmed binding sites of TFs. These events are located at 107 loci next to 130 genes and could be observed across the phylogenetic tree, with some events that occurred independently several times. We further focused on 2 genes that showed the longest IR expansion and created IR-expanded mutants in the BY4741 lab strain. While the expansion did not change much at the ERT1 gene, the gre2 mutant with IR expansion was very different from BY4741. In the GRE2 IR-expanded mutant, GRE2 expression was higher than in wild-type; the mutant grew more slowly but was relatively more resistant to glycolaldehyde, a substrate of Gre2p. Taken together, we show here that IR-expansion at promoters is frequent and can shape the evolution of transcription regulation.