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, Malgorzata Rowicka-Kudlicka, Ivan Dikic

Research output: Contribution to journalArticle

170 Citations (Scopus)

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 2013

Fingerprint

Double-Stranded DNA Breaks
Aphidicolin
Nucleotides
Genes
DNA
Genome
Streptavidin
Chromosome Mapping
Endonucleases
Neoplasm Genes
Telomere
Labeling
Cells
Satellites
Neoplasms

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Crosetto, N., Mitra, A., Silva, M. J., Bienko, M., Dojer, N., Wang, Q., ... 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

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. / Crosetto, Nicola; Mitra, Abhishek; Silva, Maria Joao; Bienko, Magda; Dojer, Norbert; Wang, Qi; Karaca, Elif; Chiarle, Roberto; Skrzypczak, Magdalena; Ginalski, Krzysztof; Pasero, Philippe; Rowicka-Kudlicka, Malgorzata; Dikic, Ivan.

In: Nature Methods, Vol. 10, No. 4, 04.2013, p. 361-365.

Research output: Contribution to journalArticle

Crosetto, N, Mitra, A, Silva, MJ, Bienko, M, Dojer, N, Wang, Q, Karaca, E, Chiarle, R, Skrzypczak, M, Ginalski, K, Pasero, P, Rowicka-Kudlicka, M & Dikic, I 2013, 'Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing', Nature Methods, vol. 10, no. 4, pp. 361-365. https://doi.org/10.1038/nmeth.2408
Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N, Wang Q et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nature Methods. 2013 Apr;10(4):361-365. https://doi.org/10.1038/nmeth.2408
Crosetto, Nicola ; Mitra, Abhishek ; Silva, Maria Joao ; Bienko, Magda ; Dojer, Norbert ; Wang, Qi ; Karaca, Elif ; Chiarle, Roberto ; Skrzypczak, Magdalena ; Ginalski, Krzysztof ; Pasero, Philippe ; Rowicka-Kudlicka, Malgorzata ; Dikic, Ivan. / Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. In: Nature Methods. 2013 ; Vol. 10, No. 4. pp. 361-365.
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