The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single-nucleotide polymorphisms in the bovine genome.
Bayesian analysis was performed to examine the single-nucleotide polymorphism (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) C <--> T and A <--> G transitions have reverse complementary neighborhood patterns and so do A <--> C and G <--> T transversions. Our 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 C <--> T/A <--> G and A <--> C/G <--> T, the true neighborhood patterns for A <--> T and C <--> G 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 C <--> G, but increased for C <--> T/A <--> G, further for A <--> C/G <--> T, and the most for A <--> T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A <--> G and C <--> T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for approximately 20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.
Jiang
Zhihua
Z
Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351, USA. jiangz@wsu.edu
Wu
Xiao-Lin
XL
Zhang
Ming
M
Michal
Jennifer J
JJ
Wright
Raymond W
RW
D000818:Animals; D001499:Bayes Theorem; D002417:Cattle; D003165:Complement System Proteins; D018899:CpG Islands; D019175:DNA Methylation; D004252:DNA Mutational Analysis; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D016678:Genome; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D011336:Probability
D003165:Complement System Proteins