ArticleNature methods2021
Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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Who cites it
43 citing papers in PubMed.
- Translating base editors: a decade of progress from the bench to the clinic.Nature reviews. Drug discovery · 2026Review
- Base editing for precision therapeutics.Cell genomics · 2026Review
- Tracking-seq: a universal off-target detection approach for CRISPR-Cas genome editing.Nature protocols · 2026Review
- Ultra-sensitive profiling of CRISPR-Cas off-target effects with Tracking-seq2.Nature communications · 2026Article
- Article
- The future of pediatric gene therapy: CRISPR-Cas9, AI, and personalized medicine.Pediatric research · 2026Review
- High-precision cytosine base editors by evolving nucleic-acid-recognition hotspots in deaminase.Nature biotechnology · 2026Article
- Base editing both DNA strands in distinct editing windows with small CRISPR-associated effector Cas12f1.iScience · 2025Article
- Noncanonical target-strand cytosine base editing via engineered Un1Cas12f1 platform.Nature communications · 2025Article
- TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors.Nature chemical biology · 2025Article
- Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells.bioRxiv : the preprint server for biology · 2025Article
- Review
- Charting the development and engineering of CRISPR base editors: lessons and inspirations.Cell chemical biology · 2025Review
- Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing.Nature biotechnology · 2025Article
- A comprehensive benchmark for multiple highly efficient base editors with broad targeting scope.bioRxiv : the preprint server for biology · 2025Article
- Selict-seq profiles genome-wide off-target effects in adenosine base editing.Nucleic acids research · 2025Article
- Improving adenine base editing precision by enlarging the recognition domain of CRISPR-Cas9.Nature communications · 2025Article
- Advancements of CRISPR-Mediated Base Editing in Crops and Potential Applications inInternational journal of molecular sciences · 2024Review
- Tracking endogenous proteins based on RNA editing-mediated genetic code expansion.Nature chemical biology · 2024Article
- CRISPR/Cas9-mediated base editors and their prospects for mitochondrial genome engineering.Gene therapy · 2024Review
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytosine base editors (CBEs) have the potential to correct human pathogenic point mutations. However, their genome-wide specificity remains poorly understood. Here we report Detect-seq for the evaluation of CBE specificity. It enables sensitive detection of CBE-induced off-target sites at the genome-wide level. Detect-seq leverages chemical labeling and biotin pulldown to trace the editing intermediate deoxyuridine, thereby revealing the editome of CBE. In addition to Cas9-independent and typical Cas9-dependent off-target sites, we discovered edits outside the protospacer sequence (that is, out-of-protospacer) and on the target strand (which pairs with the single-guide RNA). Such unexpected off-target edits are prevalent and can exhibit a high editing ratio, while their occurrences exhibit cell-type dependency and cannot be predicted based on the sgRNA sequence. Moreover, we found out-of-protospacer and target-strand edits nearby the on-target sites tested, challenging the general knowledge that CBEs do not induce proximal off-target mutations. Collectively, our approaches allow unbiased analysis of the CBE editome and provide a widely applicable tool for specificity evaluation of various emerging genome editing tools.
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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.