Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification

By Morgan L. Maeder, Stacey Thibodeau-Beganny, A. Osiak, David A Wright, Reshma M. Anthony, Magdalena Eichtinger, Tao Jiang, Jonathan E. Foley, Ronnie J. Winfrey, J. Townsend and 16 more. Molecules and Cells, 2008

752 citations recorded by the source corpus.

Summary Custom-made zinc-finger nucleases (ZFNs) can induce targeted genome modifications with high efficiency in cell types including Drosophila, C. elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation of highly specific engineered zinc-finger arrays. Here we describe OPEN (Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multi-finger arrays, which we show is more effective than the previously published modular assembly method. We used OPEN to construct 37 highly active ZFN pairs which induced targeted alterations with high efficiencies (1 to 50%) at 11 different target sites located within three endogenous human genes (VEGF-A, HoxB13, CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally-integrated EGFP reporter gene. In summary, OPEN provides an “open-source” method for rapidly engineering highly active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN technology for biological research and gene therapy.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/122fcd15d7232f44dde07f905a01261d16a97a07

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Citations in the corpus

TALENs: a widely applicable technology for targeted genome editing (2012, neutral): “Additional methods that explicitly account for context-dependent effects among zinc fingers in an array include: Oligomerized Pool Engineering ( OPEN ) 90 , Context-Dependent Assembly ( CoDA ) 52 , and a bacterial one-hybrid ( B1H ) selection-based system 37 .”
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting (2011, background): “For example, one of the most common mutations in patients with cystic fibrosis is a deletion of 3 nt (DF508) in CFTR; however, best efforts to engineer a ZFN for this position only succeeded in targeting a site >120 bp away, a distance that would likely compromise gene targeting efficiency (18).”
Genome editing with engineered zinc finger nucleases (2010, methodology): “, and the robustness of this approach is demonstrated by its successful application to three additional human genes in transformed cell”
New plant breeding techniques. State-of-the-art and prospects for commercial development (2011, methodology): “The ZFN-1 technique has been used as an efficient mutagenesis method in Arabidopsis, tobacco and maize (Lloyd et al., 2005; Maeder et al., 2008; Shukla et al., 2009; Tovkach et al., 2009).”
A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions (2012, methodology): “Using the OPEN platform, we construct a library of speciﬁc and orthogonal sTF-promoter pairs, and demonstrate that these pairs can be used to wire synthetic transcriptional cascades in Saccharomyces cerevisiae .”
Development and Applications of CRISPR-Cas9 for Genome Engineering (2014, neutral): “ZF domains, on the other hand, exhibit context-dependent binding preference due to crosstalk between adjacent modules when assembled into a larger array (Maeder et al., 2008).”
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN] (2015, methodology): “Nature 335: 563–564 Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, et al (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).”
Genome Engineering With Zinc-Finger Nucleases (2011, background): “Methods for selecting new three-finger sets from partially randomized libraries have been developed (Meng et al. 2007; Maeder et al. 2008), but can be quite time-consuming.”
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool (2010, methodology): “All published OPEN pools currently available from the Zinc Finger Consortium are checked by default (7).”