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MBE Advance Access published online on October 20, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl156
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 17, 2006

Letter

Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions

Zhongming Zhao 1 * and Cizhong Jiang 1

1 Virginia Institute for Psychiatric and Behavioral Genetics and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA

* To whom correspondence should be addressed.
Zhongming Zhao, E-mail: zzhao{at}vcu.edu


  Abstract

Recently, Fryxell and Moon (2005) examined methylation-dependent transition rates (5mC deamination rates), which were calculated by the difference between the CpG transition and GpC transition rates, using 4,437 transition mutations in CpG or GpC dinucleotides. They concluded that 5mC deamination rates were highly dependent on local GC content but not on local sequence lengths over which GC content was calculated or the genomic regions where the mutations occurred. Here, we reexamined these statements by using 292,216 CpG->TpG/CpA and GpC->GpT/ApC mutations, an increase of 66 times as much data. Contrary to Fryxell and Moon's conclusions, our analysis indicated that 5mC deamination rates in the human genome were dependent on both the local sequence length and the genomic region. Some explanations for their conclusions were provided.

Keywords: CpG; GpC; mutation rate; single nucleotide polymorphisms; GC content; genomic regions.
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[Abstract] [Full Text] [PDF]


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