Negative correlation of G+C content at silent substitution sites between orthologous human and mouse protein-coding sequences.
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.
Takahashi
Naoki
N
Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology Division of Health Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Japan.
Nakashima
Hiroshi
H
D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition; D002874:Chromosome Mapping / Q000379:methods; D014644:Genetic Variation; D006801:Humans; D020782:Matrix Metalloproteinases / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D017354:Point Mutation / Q000502:physiology*; D017386:Sequence Homology, Amino Acid; D044502:Thymine DNA Glycosylase / Q000235:genetics
D044502:Thymine DNA Glycosylase; C117705:MMP23B protein, human; D020782:Matrix Metalloproteinases