Trends in Genetics
Volume 19, Issue 7, July 2003, Pages 365-369
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Genome Analysis
Strand misalignments lead to quasipalindrome correction

https://doi.org/10.1016/S0168-9525(03)00136-7Get rights and content

Abstract

Quasipalindromes, or imperfect inverted repeats, undergo spontaneous mutation to more-perfect inverted repeats. These mutations have been observed in many organisms, ranging from bacteria to humans, where they are associated with mutations leading to disease. We determined the relative frequency of quasipalindromes and perfect palindromes in more than 100 sequenced prokaryotic genomes. In nearly all cases, perfect palindromes were relatively more frequent than quasipalindromes, suggesting that quasipalindrome correction is a general mechanism for mutation in prokaryotes.

Section snippets

Frequency of quasipalindromes within complete genomes

One would expect that correction of quasipalindromes over a period of time should result in an increase in the frequency of perfect palindromes within the bacterial genome. The repetitiveness of genomes has been investigated before [8], as well as frequencies of specific repeats in single genomes 9, 10. Here we test sequenced bacterial genomes for the frequencies of quasipalindromes and perfect palindromes, and compare them with expected values. In Fig. 3, we show that the relative frequencies

Cruciform atlases for localization of palindromes with genomes

Palindromes are not homogeneously distributed throughout the chromosome, and the localization of quasipalindromes and perfect palindromes can be plotted in a ‘DNA atlas’ format, as described previously 13, 14, 15. Figure 5 shows a cruciform atlas for Bacillus anthracis plasmid pX01 [16]. The left-hand side of the figure has a higher fraction of palindromes than the rest of the genome. This region contains a 44 800-bp pathogenicity island, located between the two IS1627 insertion sequence (IS)

Potential for DNA directed mutational change at quasipalindrome

Quasipalindrome correction mutations constitute one class of mutation hotspot. The DNA symmetry elements allow the formation of DNA secondary structures that promote mutation. In addition, the inverted repeat nature of the sequence provides the opportunity that during leading strand replication of the quasipalindrome, a second complementary copy of the template exists in single stranded form in the lagging strand template, which might also contribute to the high frequency of mutation at

Acknowledgements

Support for research on quasipalindrome corrections mutations was provided by grant ES 05508 from the National Institute of Environmental Health Sciences, National Institutes of Health to R.R.S. D.W.U. and P.W. are supported by a grant from the Danish Research Foundation. Work in the W.A.R. laboratory is supported by a grant from the Bovaird Center for Studies in Molecular Biology and Biotechnology. The authors thank Hans Henrik Stærfeldt, Lars Juhl Jensen and Jacob L. Reimers for their help.

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