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OJBTM
Online Journal of Bioinformatics©
Volume 10 (1):165-, 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- 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.