Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing
Open accessAbstract
We present a genome-wide approach to map DNA double-strand breaks (DSBs) at nucleotide resolution by a method we termed BLESS (direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing). We validated and tested BLESS using human and mouse cells and different DSBs-inducing agents and sequencing platforms. BLESS was able to detect telomere ends, Sce endonuclease-induced DSBs and complex genome-wide DSB landscapes. As a proof of principle, we characterized the genomic landscape of sensitivity to replication stress in human cells, and we identified >2,000 nonuniformly distributed aphidicolin-sensitive regions (ASRs) overrepresented in genes and enriched in satellite repeats. ASRs were also enriched in regions rearranged in human cancers, with many cancer-associated genes exhibiting high sensitivity to replication stress. Our method is suitable for genome-wide mapping of DSBs in various cells and experimental conditions, with a specificity and resolution unachievable by current techniques.
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BLESS demonstrates a false positive rate lower than 1%.
“BLESS demonstrates a false positive rate lower than 1% (Crosetto et al., 2013; Yan et al., 2017; Kim et al., 2019), validating the accuracy of this method.”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Crosetto et al., 2013
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- Authors
- Crosetto, N., Mitra, A., Silva, M. J., Bienko, M., Dojer, N., Wang, Q., Karaca, E., Chiarle, R., Skrzypczak, M., Ginalski, K., Pasero, P., Rowicka, M., & Dikic, I.
- Affiliations
- Goethe University Frankfurt (DE)
- The University of Texas Medical Branch at Galveston (US)
- Boston Children's Hospital (US)
- University of Warsaw (PL)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Crosetto, Nicola
- Rowicka, Maga
- ORCID
- Venue
- Nature Methods
- Published
- 2013-03-17
- Volume
- 10
- Issue
- 4
- Pages
- 361-365
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3651036
- OpenAlex
- W2095950258
- Cited by
- 465
- References
- 41
- Citations by year
- 2026: 11 · 2025: 28 · 2024: 20 · 2023: 39 · 2022: 35 · 2021: 45 · 2020: 66 · 2019: 52 · 2018: 35 · 2017: 53 · 2016: 47 · 2015: 19 · 2014: 12 · 2013: 3
- FWCI
- 12.08
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- HAL (submittedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion)
- Funders
- National Institutes of Health (UL1TR000071)
- National Center for Research Resources (UL1RR029876)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- DNA double-strand breaks, telomeres, replication stress, satellite repeats, cancer genes
- MeSH terms
- Animals, Base Sequence, Cloning, Molecular, DNA Replication, Fibroblasts, Humans, Male, Mice, Inbred C57BL, Spleen, Testis, Virus Replication, Aphidicolin, Sequence Analysis, DNA, Microsatellite Repeats, Physical Chromosome Mapping, Nucleic Acid Amplification Techniques, Genomics, Cell Line, Tumor, Mice, DNA Breaks, Double-Stranded
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