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Evolution of  cis -regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of  cis -regulatory variants responsible for expression differences within and between species. While much progress has been made in relating  cis -regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of  cis -regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between  Saccharomyces  species during the diauxic shift and found appreciable  cis -acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and 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 characterized  cis -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 in  cis -regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of  cis -regulatory sequences.

Cis -regulatory variants affect gene expression dynamics in yeast