ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms

dc.contributor.author Reyon, Deepak
dc.contributor.author Kirkpatrick, Jessica
dc.contributor.author Sander, Jeffry
dc.contributor.author Zhang, Feng
dc.contributor.author Voytas, Daniel
dc.contributor.author Dobbs, Drena
dc.contributor.author Joung, J Keith
dc.contributor.author Coffman, Clark
dc.contributor.department Genetics, Development and Cell Biology
dc.contributor.department Bioinformatics and Computational Biology
dc.date 2018-02-18T04:49:58.000
dc.date.accessioned 2020-06-30T04:02:54Z
dc.date.available 2020-06-30T04:02:54Z
dc.date.copyright Sat Jan 01 00:00:00 UTC 2011
dc.date.issued 2011-01-01
dc.description.abstract <p>Background: Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN) method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by creating a user-friendly interface that identifies and provides quality scores for all potential ZFN target sites in the complete genomes of several model organisms.</p> <p>Description: ZFNGenome is a GBrowse-based tool for identifying and visualizing potential target sites for OPENgenerated ZFNs. ZFNGenome currently includes a total of more than 11.6 million potential ZFN target sites, mapped within the fully sequenced genomes of seven model organisms; S. cerevisiae, C. reinhardtii, A. thaliana, D. melanogaster, D. rerio, C. elegans, and H. sapiens and can be visualized within the flexible GBrowse environment. Additional model organisms will be included in future updates. ZFNGenome provides information about each potential ZFN target site, including its chromosomal location and position relative to transcription initiation site(s). Users can query ZFNGenome using several different criteria (e.g., gene ID, transcript ID, target site sequence). Tracks in ZFNGenome also provide “uniqueness” and ZiFOpT (Zinc Finger OPEN Targeter) “confidence” scores that estimate the likelihood that a chosen ZFN target site will function in vivo. ZFNGenome is dynamically linked to ZiFDB, allowing users access to all available information about zinc finger reagents, such as the effectiveness of a given ZFN in creating double-stranded breaks.</p> <p>Conclusions: ZFNGenome provides a user-friendly interface that allows researchers to access resources and information regarding genomic target sites for engineered ZFNs in seven model organisms. This genome-wide database of potential ZFN target sites should greatly facilitate the utilization of ZFNs in both basic and clinical research. ZFNGenome is freely available at: http://bindr.gdcb.iastate.edu/ZFNGenome or at the Zinc Finger Consortium website: http://www.zincfingers.org/.</p>
dc.description.comments <p>This article is from <em>BMC Genomics </em>12 (2011): 83, doi: <a href="http://dx.doi.org/10.1186/1471-2164-12-83" target="_blank">10.1186/1471-2164-12-83</a>. Posted with permission.</p>
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dc.identifier archive/lib.dr.iastate.edu/gdcb_las_pubs/93/
dc.identifier.articleid 1099
dc.identifier.contextkey 9739523
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath gdcb_las_pubs/93
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/38007
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/gdcb_las_pubs/93/2011_Dobbs_ComprehensiveResource.pdf|||Sat Jan 15 02:31:12 UTC 2022
dc.source.uri 10.1186/1471-2164-12-83
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Cell and Developmental Biology
dc.subject.disciplines Computational Biology
dc.subject.disciplines Genetics and Genomics
dc.title ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms
dc.type article
dc.type.genre article
dspace.entity.type Publication
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