A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes
A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes
复制标题
密码子替换模型，综合了 GC 含量、基因密度和人类染色体 CpG 岛密度的影响
作者：
K. Misawa
背景建立密码子替换模型是蛋白质序列分析的基础。最近对人类基因组非编码区突变率的研究表明，CpG突变率与局部GC含量和功能元件密度呈负相关。本研究旨在了解基因组特征，即GC含量，基因密度和CpG岛频率对人类染色体密码子替换率的影响。和非人类的CpG转换和颠换是通过比较数千个人类和黑猩猩基因的编码区来估计的，使用猕猴基因作为外群。由于基因组特征是相互依赖的，因此得到了这些特征的偏回归系数。结论密码子的替换率依赖于染色体的基因密度。转录相关突变就是这样一种压力。在这些结果的基础上，结合基因组特征对人类染色体密码子替换的影响，开发了一个密码子替换模型。
BackgroundDeveloping a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes.ResultsCodon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained.ConclusionThe substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.
影响因子：
7
作者：
Walser, Jean-Claude;Ponger, Loic;Furano, Anthony V.
通讯作者：
Furano, Anthony V.