Substitution Rate and Structural Divergence of 5′UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs

Abstract

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 (K5UTR) averaged approximately 10%-20% lower than the synonymous substitution rate (Ks). However, both the K5UTR and nonsynonymous substitution rate (Ka) were significantly higher in the testicular cDNAs than in the brain cDNAs, whereas the Ks 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 K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5'UTR sequences.

Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome

“…In a comparative study between human and cynomolgus monkey (macaque), the number of substitutions per site in the 5′-UTRs was smaller than those in the synonymous sites (Osada et al, 2005). In the present study, we also found that the numbers of substitutions per site in both the 5′-and 3′-UTRs were smaller than those in the synonymous sites, comparing human and chimpanzee (Fig.…”

Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids

“…The PCR products were cloned into pUC18 plasmids and the sequences of ≈10 clones from each library were then determined (AB249666; AB250297; AB265818; AB265819). Macaca fascicularis cDNA clones, QtsA-12626 (AB070082) and QtsA-16374 (AB070082), were isolated from the oligo-capped cDNA library described previously (Osada et al, 2005). The DNA samples were sequenced using an ABI 310 and 3730 sequencer (Applied Biosystems).…”

“…Chimpanzee testis sample was collected from an eight-year-old male chimpanzee (P. troglodytes verus) which died of natural causes. Total RNA samples of the cynomolgus monkey were obtained as described previously (Osada et al, 2005). One microgram of total mRNA was amplified using a One Step RNA PCR Kit (TakaraBio).…”

“…In the course of our transcriptome analysis of the macaque testis (Osada et al, 2005), we found that one of the genes, which showed homology to yeast gene CDC50, was expressed in macaques but not completely expressed in humans. In mammals, three types of CDC50 paralogs have been identified: transmembrane protein 30A (CDC50A or TMEM30A), 30B (CDC50B or TMEM30B), and 30C (CDC50C or TMEM30C).…”

No accelerated evolution of 3′UTR region in human for brain-expressed genes

“…On the other hand, according to previous studies, the average length of 3′UTRs is 2 kb, but the length of most of the cisregulation elements is usually short, about 10-100 bp (Gavis et al, 1996;Ewa et al, 2001;Goldberg-Cohen et al, 2002;Osada et al, 2005), which makes the detection of natural selection of the 3′UTRs less sensitive using the K 3u /K s method since it is an average value. In addition, though the general evolutionary pattern of 3′UTR of brain-expressed genes supports neutral evolution, it is still possible that a small faction of the neurofunction related genes evolved rapidly during primate evolution and have a major contribution to the brain functional divergence between human and nonhuman primates since a regulatory gene acting on the upstream of a pathway could influence the expression of a lot of downstream genes.…”