Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences
文献类型:期刊论文
作者 | Zhao ZM*1,2,3; Zhang FK1; zzhao@vcu.edu |
刊名 | Genomics |
出版日期 | 2006 |
卷号 | 87期号:X页码:69-74 |
关键词 | Single Nucleotide Polymorphisms Snps Short Sequence Mouse Human Cpg Islands Cpg Dinucleotide Cpg Effect |
英文摘要 |
A genome-wide view of sequence mutability in mice is still limited, although biologists usually assume the same scenario for mice as for
humans. In this study, we examined the sequence context in the local environment of 482,528 mouse single nucleotide polymorphisms (SNPs).
We found that CpG-containing short sequences, in general, had more representation in the local sequences of SNPs compared to the genome
sequences. The extent of this overrepresentation was stronger in mice than in humans, which is inconsistent with previous observations of the
weaker neighboring-nucleotide biases on mouse SNPs. To exclude the CpG effect, we compared the distribution patterns of short sequences
among the six categories of SNPs. The results revealed an even stronger pattern in the CpG-containing group for C/G substitution compared to for
A/G or C/Tsubstitutions. We next performed the first genome-wide sequence context analysis of SNPs in the mouse CpG islands. SNPs occurring
at CpG sites were 3.14-fold less prevalent than expected, suggesting the suppression of methylation-dependent deamination in the CpG islands.
The extent of this suppression was less in mice than in humans. Finally, compared with humans, the observations of a greater deficit of CpG
dinucleotides, a stronger overrepresentation of CpG-containing n-mers surrounding the polymorphic sites, and a higher SNP/genome ratio of CpG
dinucleotides in the mouse genome support the ‘‘loss of CpG islands’’ model in the mouse lineage. |
语种 | 英语 |
资助机构 | This project was supported by the A.D. Williams Trust Funds and the Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by the A.D. Williams Trust Funds and the Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by the A.D. Williams Trust Funds and the Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by the A.D. Williams Trust Funds and the Thomas F. and Kate Miller Jeffress Memorial Trust Fund. |
源URL | [http://159.226.149.26:8080/handle/152453/11767] |
专题 | 昆明动物研究所_其他 昆明动物研究所_细胞与分子进化重点实验室 |
通讯作者 | zzhao@vcu.edu |
作者单位 | 1.Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA 2.Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA 3.Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China |
推荐引用方式 GB/T 7714 | Zhao ZM*,Zhang FK,zzhao@vcu.edu. Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences[J]. Genomics,2006,87(X):69-74. |
APA | Zhao ZM*,Zhang FK,&zzhao@vcu.edu.(2006).Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences.Genomics,87(X),69-74. |
MLA | Zhao ZM*,et al."Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences".Genomics 87.X(2006):69-74. |
入库方式: OAI收割
来源:昆明动物研究所
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