Takahashi Naoki, Nakashima Hiroshi
Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology Division of Health Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Japan.
DNA Res. 2006 Aug 31;13(4):135-40. doi: 10.1093/dnares/dsl007. Epub 2006 Oct 17.
We conducted a genome-wide analysis of variations in guanine plus cytosine (G+C) content at the third codon position at silent substitution sites of orthologous human and mouse protein-coding nucleotide sequences. Alignments of 3776 human protein-coding DNA sequences with mouse orthologs having >50 synonymous codons were analyzed, and nucleotide substitutions were counted by comparing sequences in the alignments extracted from gap-free regions. The G+C content at silent sites in these pairs of genes showed a strong negative correlation (r = -0.93). Some gene pairs showed significant differences in G+C content at the third codon position at silent substitution sites. For example, human thymine-DNA glycosylase was A+T-rich at the silent substitution sites, while the orthologous mouse sequence was G+C-rich at the corresponding sites. In contrast, human matrix metalloproteinase 23B was G+C-rich at silent substitution sites, while the mouse ortholog was A+T-rich. We discuss possible implications of this significant negative correlation of G+C content at silent sites.
我们对直系同源的人类和小鼠蛋白质编码核苷酸序列的沉默替换位点上第三个密码子位置的鸟嘌呤加胞嘧啶（G+C）含量变异进行了全基因组分析。分析了3776条人类蛋白质编码DNA序列与具有超过50个同义密码子的小鼠直系同源序列的比对情况，并通过比较从无间隙区域提取的比对序列中的核苷酸替换来计数。这些基因对中沉默位点的G+C含量呈现出强烈的负相关（r = -0.93）。一些基因对在沉默替换位点的第三个密码子位置的G+C含量存在显著差异。例如，人类胸腺嘧啶-DNA糖基化酶在沉默替换位点富含A+T，而相应的小鼠直系同源序列在对应位点富含G+C。相反，人类基质金属蛋白酶23B在沉默替换位点富含G+C，而小鼠直系同源序列富含A+T。我们讨论了沉默位点G+C含量这种显著负相关的可能影响。
