Accumulation of<i>cis</i>- and<i>trans</i>-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species

Abstract Gene regulatory variations accumulate during evolution and alter gene expression. While the importance of expression variation in phenotypic is well established, molecular basis remains largely unknown. Here, we examine two closely related yeast species, Saccharomyces cerevisiae paradoxus, which show phenotypical differences morphology cell cycle progression when grown same environment. By profiling transcriptome binding key transcription factors (TFs) species their hybrid, that changes levels dynamics oscillating genes are dominated by upstream trans-variations. We find multiple regulators both cis- trans-regulatory variations, alters favor different phenotypes. Moreover, TFs, Fkh1, Fkh2 affect target genes, specificity an interacting TF, Ace2. Our study reveals how propagate through network, TFs binding, contributing to progression.