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

Thumbnail Image
Date
2011-01-01
Authors
Reyon, Deepak
Kirkpatrick, Jessica
Sander, Jeffry
Zhang, Feng
Voytas, Daniel
Joung, J Keith
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Authors
Person
Dobbs, Drena
University Professor Emeritus
Person
Coffman, Clark
Associate Professor
Research Projects
Organizational Units
Organizational Unit
Genetics, Development and Cell Biology

The Department of Genetics, Development, and Cell Biology seeks to teach subcellular and cellular processes, genome dynamics, cell structure and function, and molecular mechanisms of development, in so doing offering a Major in Biology and a Major in Genetics.

History
The Department of Genetics, Development, and Cell Biology was founded in 2005.

Related Units

Organizational Unit
Bioinformatics and Computational Biology
The Bioinformatics and Computational Biology (BCB) Program at Iowa State University is an interdepartmental graduate major offering outstanding opportunities for graduate study toward the Ph.D. degree in Bioinformatics and Computational Biology. The BCB program involves more than 80 nationally and internationally known faculty—biologists, computer scientists, mathematicians, statisticians, and physicists—who participate in a wide range of collaborative projects.
Journal Issue
Is Version Of
Versions
Series
Abstract

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.

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.

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/.

Comments

This article is from BMC Genomics 12 (2011): 83, doi: 10.1186/1471-2164-12-83. Posted with permission.

Description
Keywords
Citation
DOI
Copyright
Sat Jan 01 00:00:00 UTC 2011
Collections