MAIN


©1996-2009 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


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, University of Hong Kong, Pokfulam, Hong Kong


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.


MAIN

 

FULL-TEXT(SUBSCRIPTION)