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ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

Thomas J Cradick1*, Giovanna Ambrosini23, Christian Iseli24, Philipp Bucher23 and Anton P McCaffrey1

  • * Corresponding author: Thomas J Cradick tj@alum.mit.edu

  • † Equal contributors

Author Affiliations

1 University of Iowa School of Medicine, Department of Internal Medicine, Iowa City, Iowa, 52245, USA

2 Swiss Institute of Bioinformatics (SIB), Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

3 Ecole Polytechnique Federale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), 1015 Lausanne, Switzerland

4 Ludwig Institute for Cancer Research (LICR), Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

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BMC Bioinformatics 2011, 12:152  doi:10.1186/1471-2105-12-152

Published: 13 May 2011

Abstract

Background

Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not absolute; therefore, it is essential to select ZFN target sites without similar genomic off-target sites. It is important to assay for off-target cleavage events at sites similar to the target sequence.

Results

ZFN-Site is a web interface that searches multiple genomes for ZFN off-target sites. Queries can be based on the target sequence or can be expanded using degenerate specificity to account for known ZFN binding preferences. ZFN off-target sites are outputted with links to genome browsers, facilitating off-target cleavage site screening. We verified ZFN-Site using previously published ZFN half-sites and located their target sites and their previously described off-target sites. While we have tailored this tool to ZFNs, ZFN-Site can also be used to find potential off-target sites for other nucleases, such as TALE nucleases.

Conclusions

ZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.