Substitution rate and structural divergence of 5′UTR evolution: Comparative analysis between human and cynomolgus monkey cDNAs

The substitution rate and structural divergence in the 5′- untranslated region (UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in the UTR than in the coding sequence, the divergence between humans and macaques would provide a good estimate of the nucleotide substitution rate and structural divergence in the 5′UTR. We found that the substitution rate in the 5′UTR (K _5UTR) averaged ≈10%-20% lower than the synonymous substitution rate (K _s). However, both the K _5UTR and nonsynonymous substitution rate (K _a) were significantly higher in the testicular cDNAs than in the brain cDNAs, whereas the K _s did not differ. Further, an in silico analysis revealed that 27% (169/622) of macaque testicular cDNAs had an altered exon-intron structure in the 5′UTR compared with the human cDNAs. The fraction of cDNAs with an exon alteration was significantly higher in the testicular cDNAs than in the brain cDNAs. We confirmed by using reverse transcriptase-polymerase chain reaction that about one-third (6/16) of in silico "macaque-specific" exons in the 5′UTR were actually macaque specific in the testis. The results imply that positive selection increased K _5UTR and structural alteration rate of a certain fraction of genes as well as K _a. We found that both positive and negative selection can act on the 5′UTR sequences.