Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions.

Morton, Brian R.

doi:10.1073/pnas.92.21.9717

Cited by 94 publications

(92 citation statements)

References 16 publications

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“…However, the A 4 T transversions were the least frequent in humans (7.42%) and cattle (6.14%), while the C 4 G substitutions were the least frequent in mouse (6.37%) and Atlantic salmon (8%) (Hayes et al 2007). Interestingly, when two immediate adjacent sites flanking the SNPs were A 1 T rich (A 1 T content of 2, in particular), the frequency of transversional mutations significantly increased in animals, such as cattle (38.56%), human (38.70%), and mouse (36.50%), and in plants, such as Arabidopsis (53%) (Zhang and Zhao 2004) and the rice and maize chloroplast noncoding regions (57%) (Morton 1995).…”

Section: Discussionmentioning

confidence: 99%

“…It has been widely believed that the hypermutability effects of CpG dinucleotide sites contribute significantly to the increased rate of transitions in both plant and animal genomes as a result of deamination of methylated cytosines (Duncan and Miller 1980). However, the A 1 T content of the two immediate sites adjacent to the mutation sites is associated with an increased rate of transversion in the 1 nuclear genomes of human, mouse, and Arabidopsis (Zhang and Zhao 2004) as well as in the chloroplast genomes of rice and maize (Morton 1995). Interestingly, the two adjacent nucleotide sites that flank the mutations also show the largest biases compared to the genomewide and chromosome-specific average (Zhao and Boerwinkle 2002;Zhang and Zhao 2004).…”

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confidence: 97%

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The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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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 1 Tcontent equals two at their immediate adjacent sites; and (3) C 4 Tand A 4 G transitions have reverse complementary neighborhood patterns and so do A 4 C and G 4 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 4 T/ A 4 G and A 4 C/G 4 T, the true neighborhood patterns for A 4 T and C 4 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 1 T and G 1 C was quite different. The ratio was lowest for C 4 G, but increased for C 4 T/A 4 G, further for A 4 C/G 4 T, and the most for A 4 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 4 G and C 4 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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Section: Discussionmentioning

confidence: 99%

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confidence: 97%

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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“…Context dependency of mutations has also been studied in grass chloroplast DNA (cpDNA; Morton 1995Morton , 2003. In this genome there is a significant correlation between the A 1 T content of the two sites flanking a mutation (the A/T context) and both the overall substitution rate and the transition:transversion (Ts:Tv) bias, due to a decreasing rate of transition substitutions as the A/T context increases (Morton 2003).…”

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confidence: 99%

“…A number of analyses of mutations have demonstrated that context, or the composition of nucleotides flanking a mutation, can have a significant influence on both mutation bias and overall mutation rate (Bulmer 1986;Morton 1995;Krawczak et al 1998;Zhao and Boerwinkle 2002;Morton 2003). Although context effects are not often considered in studies that apply mutation parameters (although see Arndt et al 2003;Siepel and Haussler 2003), there is evidence that understanding and incorporating such effects may be very important for interpreting genomic data (Morton 2003;Siepel and Haussler 2003) since they can result in variation in mutation dynamics across sites.…”

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confidence: 99%

Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition

Morton

McMullen

et al. 2006

Genetics

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We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A 1 T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC / AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A 1 T content, ranging from a 1.7-fold increase in transition rate in relatively G 1 C-rich regions to a 2.6-fold increase in A 1 T-rich regions. We also observe a relationship between locus A 1 T content and GC / AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC / AT pressure increases with increasing locus A 1 Tcontent but decreases with increasing flanking base A 1 T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.

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“…However, in humans previous analyses of SNP variation and neighboringnucleotide effects have largely been limited to pseudogenes or a limited number of genes with known effects, many of which are disease-causing (e.g., Gojobori et al 1982;Li et al 1984;Cooper and Krawczak 1990;Krawczak et al 1998). In plants, effects of neighboring nucleotides have been extensively studied in chloroplasts (e.g., Morton 1995;Morton et al 1997).…”

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confidence: 99%

Neighboring-Nucleotide Effects on Single Nucleotide Polymorphisms: A Study of 2.6 Million Polymorphisms Across the Human Genome

2002

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We investigated substitution patterns and neighboring-nucleotide effects for 2,576,903 single nucleotide polymorphisms (SNPs) publicly available through the National Center for Biotechnology Information (NCBI). The proportions of substitutions were A/G, 32.77%; C/T, 32.81%; A/C, 8.98%; G/T, 9.06%; A/T, 7.46%; and C/G, 8.92%. The two nucleotides immediately neighboring the variable site showed major deviation from genome-wide and chromosome-specific expectations, although lesser biases extended as far as 200 bp. On the 5′ side, the biases for A, C, G, and T were 1.43%, 4.91%, −1.70%, and −4.62%, respectively. These biases were −4.44%, −1.59%, 5.05%, and 0.99%, respectively, on the 3′ side. The neighboring-nucleotide patterns for transitions were dominated by the hypermutability effects of CpG dinucleotides. Transitions were more common than transversions, and the probability of a transversion increased with increasing A + T content at the two adjacent sites. Neighboring-nucleotide biases were not consistent among chromosomes, with Chromosomes 19 and 22 standing out as different from the others. These data provide genome-wide information about the effects of neighboring nucleotides on mutational and evolutionary processes giving rise to contemporary patterns of nucleotide occurrence surrounding SNPs

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Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions.

Cited by 94 publications

References 16 publications

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition

Neighboring-Nucleotide Effects on Single Nucleotide Polymorphisms: A Study of 2.6 Million Polymorphisms Across the Human Genome

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