Journal Article

Negative Correlation of G+C Content at Silent Substitution Sites Between Orthologous Human and Mouse Protein-Coding Sequences

Naoki Takahashi and Hiroshi Nakashima

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 13, issue 4, pages 135-140
Published in print October 2006 | ISSN: 1340-2838
Published online January 2006 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsl007

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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.

Keywords: G+C content variation; human–mouse orthologs; nucleotide substitutions in synonymous codons

Journal Article.  2743 words.  Illustrated.

Subjects: Genetics and Genomics

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