Variation in cis-regulatory sequences has been shown to modulate gene expression levels or developmental patterns. However, temporal control of gene expression may be as important to fitness as steady-state levels. To determine whether cis-regulatory sequence variation contributes to gene expression dynamics as well as steady-state levels we measured allele-specific expression within multiple yeast hybrids during the transition from fermentative to respiratory growth.
We found 961-3045 genes with allele-specific differences in expression that changed over time. In comparison, we found 466-863 genes with allele-specific differences in expression either during growth on glucose or ethanol. Using logistic regression, we found that single nucleotide polymorphisms (SNPs) in promoters regions are associated with a 1.02-1.04 odds ratio (OR) of allele specific expression. In contrast, insertions and deletions (InDels) are associated with a 1.11-1.15 OR of allele-specific expression.
We conclude that there is nearly as much cis-acting variation that affects temporal changes in gene expression as affects steady-state levels alone. Our observation that InDels have a stronger association than SNPs suggests a difference in how expression levels and dynamics are modulated.