Cis-regulatory variants affect gene expression dynamics in yeast

Evolution ofcis-regulatory sequences depends on how they effect gene expression and motivates both the identification and prediction ofcis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relatingcis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution ofcis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and betweenSaccharomycesspecies during the diauxic shift and found appreciablecis-acting variation in gene expression dynamics. Within species ASE is associated with intergenic variants, but ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression we identified and characterizedcis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes incis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects expression are relevant to the evolution ofcis-regulatory sequences.