ArticleNature biotechnology2011
An unbiased genome-wide analysis of zinc-finger nuclease specificity.
Article in Nature biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 281 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
281 citing papers in PubMed.
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- Gene therapy for huntington's disease: advances, challenges, and future perspectives.Neurogenetics · 2026Review
- Design principle of successful genome editing applications using CRISPR-based toolkits.Journal of applied genetics · 2025Review
- Precise Mapping of Physiological DSBs Using In-Suspension Break Labeling In Situ and Sequencing (sBLISS).Methods in molecular biology (Clifton, N.J.) · 2025Article
- Emerging Gene-editing nano-therapeutics for Cancer.Heliyon · 2024Review
- Advances in the labelling and selective manipulation of synapses.Nature reviews. Neuroscience · 2024Review
- Viral and nonviral nanocarriers forNano research · 2024Article
- Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond.JACS Au · 2024Review
- Progress and Prospects of Gene Editing in Pluripotent Stem Cells.Biomedicines · 2023Review
- Correcting inborn errors of immunity: From viral mediated gene addition to gene editing.Seminars in immunology · 2023Review
- Beyond the promise: evaluating and mitigating off-target effects in CRISPR gene editing for safer therapeutics.Frontiers in bioengineering and biotechnology · 2023Review
- Off-target effects in CRISPR/Cas9 gene editing.Frontiers in bioengineering and biotechnology · 2023Review
- Choice of template delivery mitigates the genotoxic risk and adverse impact of editing in human hematopoietic stem cells.Cell stem cell · 2022Article
- Site-specific genome editing in treatment of inherited diseases: possibility, progress, and perspectives.Medical review (2021) · 2022Review
- Article
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.Genome biology · 2022Article
- Improved alpharetrovirus-based Gag.MS2 particles for efficient and transient delivery of CRISPR-Cas9 into target cells.Molecular therapy. Nucleic acids · 2022Article
- Disruption of HIV-1 co-receptors CCR5 and CXCR4 in primary human T cells and hematopoietic stem and progenitor cells using base editing.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Hematopoietic stem and progenitors cells gene editing: Beyond blood disorders.Frontiers in genome editing · 2022Review
- Article
221 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Zinc-finger nucleases (ZFNs) allow gene editing in live cells by inducing a targeted DNA double-strand break (DSB) at a specific genomic locus. However, strategies for characterizing the genome-wide specificity of ZFNs remain limited. We show that nonhomologous end-joining captures integrase-defective lentiviral vectors at DSBs, tagging these transient events. Genome-wide integration site analysis mapped the actual in vivo cleavage activity of four ZFN pairs targeting CCR5 or IL2RG. Ranking loci with repeatedly detectable nuclease activity by deep-sequencing allowed us to monitor the degree of ZFN specificity in vivo at these positions. Cleavage required binding of ZFNs in specific spatial arrangements on DNA bearing high homology to the intended target site and only tolerated mismatches at individual positions of the ZFN binding sites. Whereas the consensus binding sequence derived in vivo closely matched that obtained in biochemical experiments, the ranking of in vivo cleavage sites could not be predicted in silico. Comprehensive mapping of ZFN activity in vivo will facilitate the broad application of these reagents in translational research.
Indexed as
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.