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

Nicola Crosetto, Abhishek Mitra, Maria Joao Silva, Magda Bienko, Norbert Dojer, Qi Wang, Elif Karaca, Roberto Chiarle, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero, Maga Rowicka, Ivan Dikic

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)361-365
Number of pages5
JournalNature Methods
Volume10
Issue number4
DOIs
StatePublished - Apr 1 2013

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ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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. (2013). Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nature Methods, 10(4), 361-365. https://doi.org/10.1038/nmeth.2408