ArticleNature communications2019
Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
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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.
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Who cites it
42 citing papers in PubMed, 76 citations in OpenAlex.
- Dual-line Genome-scale CRISPR Screening Enables Robust Target Gene Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Overcoming breeding barriers with genome editing in autopolyploid crops.BMC plant biology · 2026Review
- Multilevel characterization of genome editor nuclease activity with BreakTag.Nature protocols · 2026Review
- From delivery to integration: CRISPR-mediated large insert gene editing in primary human T cells.Clinical & translational immunology · 2026Review
- The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications.International journal of molecular sciences · 2025Review
- Optimization of the Genome Editing CRISPR-Cas9 Technology in Scedosporium apiospermum.Mycopathologia · 2025Article
- Biosecurity Primitive: Polymerase X-based Genetic Physical Unclonable Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction.bioRxiv : the preprint server for biology · 2025Article
- Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag.Nature biotechnology · 2025Article
- X-CRISP: domain-adaptable and interpretable CRISPR repair outcome prediction.Bioinformatics advances · 2025Article
- How to use CRISPR/Cas9 in plants: from target site selection to DNA repair.Journal of experimental botany · 2024Review
- Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing.Nucleic acids research · 2024Article
- Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species.Nature communications · 2024Article
- Uncovering the dynamics of precise repair at CRISPR/Cas9-induced double-strand breaks.Nature communications · 2024Article
- Article
- Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier.Nature communications · 2024Article
- REV7 Monomer Is Unable to Participate in Double Strand Break Repair and Translesion Synthesis but Suppresses Mitotic Errors.International journal of molecular sciences · 2023Article
- Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering.Nucleic acids research · 2023Article
- Using a Dual CRISPR/Cas9 Approach to Gain Insight into the Role of LRP1B in Glioblastoma.International journal of molecular sciences · 2023Article
- CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping.Genome biology · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
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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.