Negative correlation of G+C content at silent substitution sites between orthologous human and mouse protein-coding sequences
Negative correlation of G+C content at silent substitution sites between orthologous human and mouse protein-coding sequences
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DOI：
10.1093/dnares/dsl007
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发表时间：
2006-08-31
期刊：
影响因子：
4.1
通讯作者：
Nakashima, Hiroshi
中科院分区：
文献类型：
--
作者：
Takahashi, Naoki;Nakashima, Hiroshi
我们进行了一个全基因组分析的鸟嘌呤加胞嘧啶（G+C）含量的变化，在第三个密码子的位置在沉默的替代位点的orthopathic人类和小鼠的蛋白质编码核苷酸序列。分析了3776个人蛋白质编码DNA序列与具有>50个同义密码子的小鼠直系同源物的比对，并通过比较从无缺口区域提取的比对中的序列来计数核苷酸取代。这两对基因沉默位点的G+C含量呈强负相关（r = -0.93）。一些基因对在沉默替换位点的第三密码子位置处的G+C含量显示出显著差异。例如，人胸腺嘧啶-DNA糖基化酶在沉默取代位点富含A+ T，而小鼠的相应位点富含G+ C。相比之下，人基质金属蛋白酶23 B是G+ C-丰富的沉默取代位点，而小鼠直系同源物是A+ T-丰富。我们讨论了这种显着的负相关性的G+C含量在沉默的网站可能产生的影响。
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.