Analysis of the PRE configuration reveals the constraints in Ste12 oligomerization in mediating pheromone-inducible transcription in Saccharomyces cerevisiae

Yeast cell mating is regulated by the transcription factor Ste12, which activates the transcription of mating genes by binding to pheromone response elements (PREs) in their promoters. PREs vary in number and position among different promoters. However, the effect of PRE organization on Ste12-promoter interactions and the possible downstream transcription of mating genes remains to be fully understood. In this study, we analyzed yeast pheromone-induced gene expression using RNA-seq transcription profiling. We retrieved the promoters of the significantly upregulated genes, focusing on the occurrence and arrangement of PREs. PPRM1 , which carries three adjacent consensus PREs, was selected as a model for investigating the relative contribution of each PRE to promoter activity through single-base mutation or deletion. We then evaluated the impact of different PRE organizations on pheromone-induced expression by altering their orientations and copy numbers. Subsequently, we proposed a model to explain the mechanism of transcriptional regulation of pheromone-inducible genes, in which the organization of PREs modulates promoter activity by influencing Ste12 oligomerization. This study paves the way for deciphering the transcriptional mechanisms of eukaryotic regulatory systems.