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Nucleic Acids Research 2006 34(8):e57; doi:10.1093/nar/gkl184
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Published online 28 April 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae

Michael Seringhaus1, Anuj Kumar2, John Hartigan3, Michael Snyder1,4 and Mark Gerstein1,5,*

1 Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA 2 Department of Molecular, Cellular and Developmental Biology and Life Sciences Institute, University of Michigan Ann Arbor, MI 48109-2216, USA 3 Department of Statistics, Yale University New Haven, CT 06520, USA 4 Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT 06520, USA 5 Program in Computational Biology and Bioinformatics, Yale University New Haven, CT 06520, USA

*To whom correspondence should be addressed: Tel: 203 432 6105; Fax: 203 432 6946; Email: mark.gerstein{at}yale.edu

Received January 11, 2006. Revised March 8, 2006. Accepted March 23, 2006.

Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed. However, many transposons preferentially insert at specific nucleotide sequences. It is unclear to what extent such bias affects their usefulness as mutagenesis tools. Here, we examine insertion site specificity and global insertion behavior of two mini-transposons previously used for large-scale gene disruption in Saccharomyces cerevisiae: Tn3 and Tn7. Using an expanded set of insertion data, we confirm that Tn3 displays marked preference for the AT-rich 5 bp consensus site TA[A/T]TA, whereas Tn7 displays negligible target site preference. On a genome level, both transposons display marked non-uniform insertion behavior: certain sites are targeted far more often than expected, and both distributions depart drastically from Poisson. Thus, to compare their insertion behavior on a genome level, we developed a windowed Kolmogorov–Smirnov (K–S) test to analyze transposon insertion distributions in sequence windows of various sizes. We find that when scored in large windows (>300 bp), both Tn3 and Tn7 distributions appear uniform, whereas in smaller windows, Tn7 appears uniform while Tn3 does not. Thus, both transposons are effective tools for gene disruption, but Tn7 does so with less duplication and a more uniform distribution, better approximating the behavior of the ideal transposon.


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