DNA Breaks and End Resection Measured Genome-wide by End Sequencing
Open accessAbstract
DNA double-strand breaks (DSBs) arise during physiological transcription, DNA replication, and antigen receptor diversification. Mistargeting or misprocessing of DSBs can result in pathological structural variation and mutation. Here we describe a sensitive method (END-seq) to monitor DNA end resection and DSBs genome-wide at base-pair resolution in vivo. We utilized END-seq to determine the frequency and spectrum of restriction-enzyme-, zinc-finger-nuclease-, and RAG-induced DSBs. Beyond sequence preference, chromatin features dictate the repertoire of these genome-modifying enzymes. END-seq can detect at least one DSB per cell among 10,000 cells not harboring DSBs, and we estimate that up to one out of 60 cells contains off-target RAG cleavage. In addition to site-specific cleavage, we detect DSBs distributed over extended regions during immunoglobulin class-switch recombination. Thus, END-seq provides a snapshot of DNA ends genome-wide, which can be utilized for understanding genome-editing specificities and the influence of chromatin on DSB pathway choice.
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END-seq used to identify strand breaks in human iPSC-derived neurons found that enhancers are hotspots for SSBs.
“a DSB‐mapping technique known as END‐seq was recently used to identify strand breaks in human induced pluripotent stem cell (iPSC)‐derived neurons, resulting in the finding that enhancers are hotspots for SSBs”
From Mechanisms of DNA damage-mediated neurotoxicity in neurodegenerative disease (2022) · cites this paper as Canela et al, 2016
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- Authors
- Canela, A., Sridharan, S., Sciascia, N., Tubbs, A., Meltzer, P., Sleckman, B. P., & Nussenzweig, A.
- Affiliations
- National Institutes of Health (US)
- Weill Cornell Medicine (US)
- Corresponding author
- Nussenzweig, André
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-09
- Volume
- 63
- Issue
- 5
- Pages
- 898-911
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC6299834
- OpenAlex
- W2495544654
- Cited by
- 284
- References
- 61
- Citations by year
- 2026: 16 · 2025: 40 · 2024: 33 · 2023: 23 · 2022: 28 · 2021: 34 · 2020: 44 · 2019: 27 · 2018: 14 · 2017: 21 · 2016: 4
- FWCI
- 11.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (Z01BC010283, Z01BC010959)
- National Institute of Allergy and Infectious Diseases (R01AI074953)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- DNA double-strand breaks, DNA end resection, restriction enzyme cleavage, zinc finger nucleases, off-target cleavage, immunoglobulin class switch recombination, genome editing specificity, base-pair resolution
- MeSH terms
- Animals, B-Lymphocytes, Chromatin, DNA, DNA Replication, DNA-Binding Proteins, Gene Expression Regulation, Histones, Recombination, Genetic, Genome, Receptors, Antigen, T-Cell, alpha-beta, Immunoglobulin Class Switching, Mice, DNA Breaks, Double-Stranded, Precursor Cells, B-Lymphoid, High-Throughput Nucleotide Sequencing, Thymocytes, Ataxia Telangiectasia Mutated Proteins
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