Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions

摘要

Recently, Fryxell and Moon (2005) examined methylation-dependent transition rates (5(m)C 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 5(m)C 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 5(m)C 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.