Effects of cis and trans regulatory variations on the expression divergence of heat shock response genes between yeast strains

► Increase of cis-variation effect on intraspecific expression divergence by heat shock ► Many genes showed the same trend of regulatory variation effect after heat stress. ► Cis variation effect was stronger in TATA box-containing genes after heat stress. ► Genes with longer intergenic region tend to show increase of trans variation effect.