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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Aphidicolin
  • Base Sequence
  • Cell Line, Tumor
  • Cloning, Molecular
  • DNA Breaks, Double-Stranded*
  • DNA Replication
  • Fibroblasts / metabolism
  • Genomics / methods*
  • Humans
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Microsatellite Repeats
  • Nucleic Acid Amplification Techniques / methods*
  • Physical Chromosome Mapping / methods
  • Sequence Analysis, DNA
  • Spleen
  • Testis
  • Virus Replication


  • Aphidicolin