Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing

By N. Crosetto, Abhishek Mitra, M. Silva, M. Bienko, Norbert Dojer, Qi Wang, E. Karaca, R. Chiarle, M. Skrzypczak, Krzysztof Ginalski and 3 more. 2013

450 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

Citations in the corpus

• Target specificity of the CRISPR-Cas9 system (2014, unknown): “Cas9 and other DNA endonucleases typically induce DSBs, and several assays have been developed to capture DSBs induced in cells [41,46,47], although none of them have been applied to the Cas9 system.”
• Development and Applications of CRISPR-Cas9 for Genome Engineering (2014, unknown): “…analysis at multiple target sites could be a high-throughput solution for understanding binding degeneracy (Wu et al., 2014), whereas techniques for detecting and labeling double-strand breaks (Crosetto et al., 2013) will help to achieve a comprehensive map of Cas9-induced off-target indels.”