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OJBTM
Online Journal of
Bioinformatics©
Volume 10 (1):165-179, 2009.
Comparative genomic study on context-dependence of CpG mutations:
Acceleration effect of 5’ T
nucleotides and new evidence of strand asymmetry in genes.
Wang Y, Leung FC
School of Biological Sciences and Genome Research
Centre,
ABSTRACT
Wang Y, Leung FC., Comparative genomic study on
context-dependence of CpG mutations: Acceleration
effect of 5’ T nucleotides and new evidence of strand asymmetry in genes,
Online J Bioinformatics 10 (2):165-179, 2009. Previous studies have reported context-dependence of CpG mutations. In this study, we demonstrate the effect of
four CpG flanking nucleotides through comparative
genomic analyses. We obtained orthologous genes of C. elegans,
fruitfly, sea squirt, zebrafish and human. Analyses
on two 5’ flanking positions reveal that T at -2 position can affect T/A to G/C
changes at -1 position more significantly than the other nucleotides. As a
co-effect of the T/A to G/C changes and CpG
mutations, TTCG motif is significantly lower than AACG motif in the zebrafish
and human genes. We then studied observed/expected values of dicodons that have a central CpG.
The value of TTC•GAA is lowest except in C. elegans,
supporting again the context-dependent effect in genes. In addition, we
calculated substitutional rates of CpG and four
flanking sites. The rate of G is much lower than that of C, and even those of
two most adjacent flanking positions for all the species. Mutational rate of CpG sites is facilitated by 5’flanking T nucleotides, and
substitutions on CpG sites in genes are more
frequently observed on sense strand.
Key
words: CpG methylation; context-dependent mutation; CpG deficiency; strand assymmetry.
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