Basal association of a transcription factor favors early gene expression

Responses to extracellular signals via Mitogen-Activated Protein Kinase (MAPK) pathways control complex transcriptional programs where hundreds of genes are induced at a desired level with a specific timing. Gene expression regulation is largely encoded in the promoter of the gene, which harbors numerous transcription factor binding sites. In the mating MAPK pathway of Saccharomyces cerevisiae, one major transcription factor, Ste12, controls the chronology of gene expression necessary for the fusion of two haploid cells. Because endogenous promoters encode a large diversity of Ste12 binding sites (PRE), we engineered synthetic promoters to decipher the rules that dictate mating gene induction. Conformations of PRE dimers that allow efficient gene expression were identified. The strength of binding of Ste12 to the PRE and the distance of the binding sites to the core promoter modulate the level of induction. The speed of activation is ensured by favoring a basal association of Ste12 by using a strong dimer of PRE located in a nucleosome depleted region. Author SummaryDuring development, cell fate decisions allow pluripotent cells to differentiate into various cell types. This process requires cells to integrate signals from their surroundings to initiate a complex transcriptional program. Budding yeasts can also undergo cell fate decisions. In presence of mating pheromones, haploid yeasts can activate a signaling pathway which can ultimately lead to the fusion of two haploid cells to form a diploid. One transcription factor, Ste12, controls this mating transcriptional program. The promoters of these 200 upregulated genes display a large diversity in the organization of Ste12 binding sites. Therefore, it is challenging to decipher how Ste12 regulates the level and the timing of gene expression. To simplify this problem, we have generated synthetic promoters, where the configuration of Ste12 binding sites on the DNA can be controlled. We have identified which conformations of binding site dimers allow a functional association of the transcription factor. In addition, we have also shown that the basal association of Ste12 to the promoter is important for the fast gene induction. An unfavorable configuration of Ste12 binding sites or the presence of nucleosomes restrict the access of the transcription factor to the DNA and results in a slower expression.