A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome

Nat Commun. 2019 Oct 24;10(1):4846. doi: 10.1038/s41467-019-12802-5.


DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes-and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage-distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents, Phytogenic / pharmacology
  • Base Sequence
  • CCCTC-Binding Factor / genetics
  • DNA / drug effects
  • DNA / metabolism*
  • DNA Breaks, Double-Stranded / drug effects
  • DNA Breaks, Single-Stranded / drug effects
  • DNA Repair*
  • DNA Topoisomerases, Type II / metabolism*
  • Endodeoxyribonucleases / metabolism*
  • Etoposide / pharmacology
  • Humans
  • Nucleotide Mapping
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*


  • Antineoplastic Agents, Phytogenic
  • CCCTC-Binding Factor
  • Saccharomyces cerevisiae Proteins
  • Etoposide
  • DNA
  • Endodeoxyribonucleases
  • Spo11 protein, S cerevisiae
  • meiotic recombination protein SPO11
  • DNA Topoisomerases, Type II