Regional and time-resolved mutation patterns of the human genome

Motivation: Substantial regional variations of substitutional processes have recently been reported from human/mouse comparisons. However, several features including the C + G dependence and the CpG-based transition effect remain obscure. Results: Utilizing the vast amount of transposable elements in the human genome, we performed detailed analysis of the substitutional and insertion/deletion patterns along the human lineage in a regional and time-resolved fashion. We observed a drastic increase in the CpG-based transition frequency at about the time of the mammalian radiation. We also observed clear regional biases of substitution patterns, most notably a bias to enrich the C+G content toward the telomeres