Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation

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  • 27 January 2003
Abstract
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. Utilizing the vast amount of repetitive sequence in the human genome, we developed a maximum likelihood approach providing estimates of substitution frequencies of the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we are able to reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around the time of the mammalian radiation (~90 Myr ago), we find an abrupt 4- to 8-fold increase of the cytosine transition rate in CpG pairs compared to that of the reptilian ancestor. Further analysis of substitutional patterns in regions with different GC-content reveals that concurrently the substitutional pattern changed from an isochore-preserving to an isochore-degrading one. We conclude that isochores have been established before the radiation of the eutherian mammals and have been subject to the process of homogenization since then.

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