Independent evolution of transcript abundance and gene regulatory dynamics

Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels, but providing limited information about variations in gene regulation. To close this gap, we profiled gene expression of related yeast species in hundreds of conditions, and used co-expression analysis to distinguish variations in transcription regulation from variations in expression levels or environmental perception. The majority of genes whose expression varied between the species maintained a conserved transcriptional regulation. Profiling the interspecific hybrid provided insights into the basis of variations, showed that trans-varying alleles interact dominantly, and revealed complementation of cis-variations by variations in trans. Our data suggests that gene expression diverges primarily through changes in promoter strength that do not alter gene positioning within the transcription network.