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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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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8978-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8979-8
Genre: Journal Article
Alternative Title : Mol Biol Evol

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 Creators:
Arndt, Peter F.1, Author              
Petrov, Dmitri A., Author
Hwa, Terence, Author
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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Free keywords: nucleotide substitution; CpG-methylation; repetitive elements; GC content
 Abstract: 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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Language(s): eng - English
 Dates: 2003-11
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 177162
DOI: 10.1093/molbev/msg204
 Degree: -

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Title: Molecular Biology and Evolution
  Alternative Title : Mol Biol Evol
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 20 (11) Sequence Number: - Start / End Page: 1887 - 1896 Identifier: ISSN: 0737-4038
ISSN: 1537-1719