Department of Genetics, Iowa State University, Ames, IA 50011, USA.
BMC Genomics. 2011 Jan 28;12:83. doi: 10.1186/1471-2164-12-83.
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.
ZFNGenome is a GBrowse-based tool for identifying and visualizing potential target sites for OPEN-generated 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.
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/.
锌指核酸酶（ZFNs）具有巨大的潜力，可以作为促进基因组修饰的工具，例如通过同源重组进行精确的基因敲除或基因替换。ZFNs 可用于推进基础研究和临床应用，包括基因治疗。最近，通过引入快速、强大且公开可用的 ZFN 设计技术，如寡聚池工程（OPEN）方法，大大提高了设计靶向任何所需基因组 DNA 序列的 ZFN 的能力。这项研究的动机是通过创建一个用户友好的界面，为使用 OPEN 生成的 ZFN 进行基因组修饰的资源，为研究人员提供更便捷的访问，该界面可以识别和提供几个模型生物完整基因组中所有潜在 ZFN 靶位点的质量评分。
ZFNGenome 是一个基于 GBrowse 的工具，用于识别和可视化 OPEN 生成的 ZFN 的潜在靶位点。ZFNGenome 目前包含超过 1160 万个潜在的 ZFN 靶位点，映射在七个模型生物的全序列基因组内；酿酒酵母、莱茵衣藻、拟南芥、黑腹果蝇、斑马鱼、秀丽隐杆线虫和智人，并且可以在灵活的 GBrowse 环境中进行可视化。未来的更新中将包括其他模型生物。ZFNGenome 提供了每个潜在 ZFN 靶位点的信息，包括其染色体位置和相对于转录起始位点的位置。用户可以使用几种不同的标准（例如，基因 ID、转录本 ID、靶位点序列）查询 ZFNGenome。ZFNGenome 中的轨迹还提供了“独特性”和 ZiFOpT（锌指 OPEN 靶向器）“置信度”评分，估计所选 ZFN 靶位点在体内发挥作用的可能性。ZFNGenome 与 ZiFDB 动态链接，使用户可以访问有关工程化 ZFN 的基因组靶位点的所有可用信息，例如给定 ZFN 在产生双链断裂方面的有效性。
ZFNGenome 提供了一个用户友好的界面，使研究人员能够访问七个模型生物中用于工程化 ZFN 的基因组靶位点的资源和信息。这个潜在 ZFN 靶位点的全基因组数据库将极大地促进 ZFN 在基础和临床研究中的应用。ZFNGenome 可在以下网址免费获取：http://bindr.gdcb.iastate.edu/ZFNGenome 或在锌指联盟网站：http://www.zincfingers.org/。
