Schorderet D F, Gartler S M
Department of Medicine, University of Washington, Seattle 98195.
Nucleic Acids Res. 1990 Dec 11;18(23):6965-9. doi: 10.1093/nar/18.23.6965.
It has been known since the development of nearest neighbor analysis that the frequency of the dinucleotide CpG is markedly suppressed in vertebrate DNA (i.e. less than %C x %G). This suppression appears to be heterogeneous since it was shown some years ago that three vertebrate tRNA genes did not exhibit CpG suppression. We have analyzed 13 different human tRNA genes and found that they also do not exhibit CpG suppression. Because CpG suppression has been linked, to some extent at least, to the methylation-deamination process by which a methylated CpG is mutated to TpG, we investigated whether the lack of suppression of CpG in tRNAs could originate from an absence of methylation. Three human tRNA genes were selected from Genbank (lysine, Proline, and Phenylalanine) and examined for methylation at HpaII sites by polymerase chain reaction (PCR) and Southern blot analysis. The observed patterns were consistent with the absence of methylation at the seven HpaII sites analyzed in and around the tRNA genes, and we predict that the remaining CpGs in these genes will be unmethylated. Since GC-rich promoter regions also escape CpG suppression and since they are generally unmethylated, avoidance of methylation may be a general explanation for the absence of CpG suppression in selected regions of vertebrate genomes.
自从最近邻分析技术发展以来，人们就已经知道在脊椎动物DNA中，二核苷酸CpG的频率受到显著抑制（即低于%C×%G）。这种抑制似乎是不均匀的，因为几年前有研究表明，三个脊椎动物的tRNA基因并未表现出CpG抑制现象。我们分析了13种不同的人类tRNA基因，发现它们同样不表现出CpG抑制。由于CpG抑制至少在一定程度上与甲基化脱氨过程相关，在此过程中，甲基化的CpG会突变为TpG，因此我们研究了tRNA中CpG缺乏抑制是否源于甲基化缺失。从基因库中选取了三个人类tRNA基因（赖氨酸、脯氨酸和苯丙氨酸），通过聚合酶链反应（PCR）和Southern印迹分析检测其在HpaII位点的甲基化情况。观察到的模式与tRNA基因内部及周围分析的七个HpaII位点不存在甲基化一致，并且我们预测这些基因中其余的CpG也将未被甲基化。由于富含GC的启动子区域也逃避了CpG抑制，且它们通常未被甲基化，因此避免甲基化可能是脊椎动物基因组特定区域缺乏CpG抑制的普遍解释。
