The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single nucleotide polymorphisms in the bovine genome

The Bayesian analysis was performed to examine the single nucleotide polymorphisms (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: 1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; 2) the transversion occurs most frequently (38.56%) in cattle when the A+T content equals two at their immediate adjacent sites and 3) CT and AG transitions have reverse complementary neighborhood patterns and so do AC and GT transversions. Our present study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike CT/AG and AC/GT, the true neighborhood patterns for AT and CG might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A+T and G+C was quite different. The ratio was lowest for CG, but increased for CT/AG, further for AC/GT and at most for AT. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Last, unequal occurrence between AG and CT in five paired neighboring structures indicates that the methylation induced deamination reactions were responsible for ~20% of total transitions. In addition, the conversion can occur at both CpG sites and non-CpG sites. Our present study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

Key Words: SNPs, methylation induced transitions, naturally occurring transitions, neighborhood patterns, reverse complement

Online ISS 1091-6490
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