Evolution of gene regulation between related species

Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, gene expression depends on conditions or cell types. Previous studies of related species described condition-specific variations in genes expression, but provided limited information aboud variations in the gene regulatory dynamics. To close this gap, we profiled the transcription program of related yeast species under hundreds of conditions. Consistent with previous reports, orthologous gene expression varies massively in each individual condition. The majority of varying genes, however, maintained a conserved regulatory dynamics, as quantified by co-expression analysis. Allele-specific profiling of inter-specific hybrid confirmed that variations in absolute expression result predominantly from cis-acting mutations. By contrast, regulatory variations are mostly due to trans-acting mutations. Our data suggests that gene expression diverges primarily through changes in promoter strength, while gene regulatory dynamics remains largely conserved.