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

Arndt, P. F., Petrov, D. A., & Hwa, T. (2003). Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Molecular Biology and Evolution, 20(11), 1887-1896. doi:10.1093/molbev/msg204.

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Genre: Zeitschriftenartikel
Alternativer Titel : Mol Biol Evol

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 Urheber:
Arndt, Peter F.1, Autor           
Petrov, Dmitri A., Autor
Hwa, Terence, Autor
Affiliations:
1Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              

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Schlagwörter: nucleotide substitution; CpG-methylation; repetitive elements; GC content
 Zusammenfassung: Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores, we develop a maximum-likelihood approach to determine the history of substitution patterns in the human genome. This approach utilizes the vast amount of repetitive sequence deposited in the human genome over the past approximately 250 Myr. Using this approach, we estimate the frequencies of seven types of substitutions: the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around 90 MYA (around the time of the mammalian radiation), we find an abrupt fourfold to eightfold increase of the cytosine transition rate in CpG pairs compared with that of the reptilian ancestor. Further analysis of nucleotide substitutions in regions with different GC content reveals concurrent changes in the substitutional patterns. Although the substitutional pattern was dependent on the regional GC content in such ways that it preserved the regional GC content before the mammalian radiation, it lost this dependence afterward. 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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Sprache(n): eng - English
 Datum: 2003-11
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: eDoc: 177162
DOI: 10.1093/molbev/msg204
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Titel: Molecular Biology and Evolution
  Alternativer Titel : Mol Biol Evol
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 20 (11) Artikelnummer: - Start- / Endseite: 1887 - 1896 Identifikator: ISSN: 0737-4038
ISSN: 1537-1719