The role of cis-regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes

Expression divergence of duplicate genes is widely believedto be important for their retention and evolution of new function,although the mechanism that determines their expression divergenceremains unclear. We use a genetical genomics approach to exploredivergence in genetical control of yeast duplicate genes createdby a whole-genome duplication that occurred about 100 MYA andthose with a younger duplication age. The analysis reveals thatduplicate genes have a significantly higher probability of sharingcommon genetic control than pairs of singleton genes. The expressionquantitative trait loci (eQTLs) have diverged completely fora high proportion of duplicate pairs, whereas a substantiallylarger proportion of duplicates share common regulatory motifsafter 100 Myr of divergent evolution. The similarity in bothgenetical control and cis motif structure for a duplicate pairis a reflection of its evolutionary age. This study revealsthat up to 20% of variation in expression between ancient duplicategene pairs in the yeast genome can be explained by both cismotif divergence (8%) and by trans eQTL divergence (10%). Initially,divergence in all 3 aspects of cis motif structure, trans-geneticalcontrol, and expression evolves coordinately with the codingsequence divergence of both young and old duplicate pairs. Thesefindings highlight the importance of divergence in both cismotif structure and trans-genetical control in the diverse setof mechanisms underlying the expression divergence of yeastduplicate genes.