Journal article
The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome
Genetics (Austin), Vol.180(1), pp.639-647
09/2008
Handle:
https://hdl.handle.net/2376/117948
PMCID: PMC2535713
PMID: 18716328
Abstract
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 ∼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.
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Details
- Title
- The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome
- Creators
- Zhihua Jiang - Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351Xiao-Lin Wu - Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351Ming Zhang - Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351Jennifer J Michal - Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351Raymond W Wright - Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351
- Publication Details
- Genetics (Austin), Vol.180(1), pp.639-647
- Academic Unit
- Animal Sciences, Department of
- Publisher
- Genetics Society of America
- Identifiers
- 99900547848501842
- Language
- English
- Resource Type
- Journal article