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Nat Methods. 2013 Apr;10(4):361-5. doi: 10.1038/nmeth.2408. Epub 2013 Mar 17.

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

Author information

1
Institute of Biochemistry II, Goethe University Medical School, Frankfurt, Germany. crosetto@mit.edu

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.

PMID:
23503052
PMCID:
PMC3651036
DOI:
10.1038/nmeth.2408
[Indexed for MEDLINE]
Free PMC Article

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