Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity

Mol Cell. 2019 Jul 25;75(2):252-266.e8. doi: 10.1016/j.molcel.2019.04.030. Epub 2019 Jun 12.


Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be "trapped" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.

Keywords: 3D chromatin organization; DNA double-strand breaks; TDP2; chromosomal translocations; cohesin; proteasome; quantitative modeling; topoisomerase; topoisomerase 2 cleavage complex; transcription.

Publication types

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

MeSH terms

  • Chromosome Breakage
  • Chromosomes / genetics
  • DNA / chemistry
  • DNA / genetics*
  • DNA Breaks, Double-Stranded*
  • DNA Repair / genetics
  • DNA Topoisomerases, Type II / chemistry*
  • DNA Topoisomerases, Type II / genetics
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • Etoposide / chemistry
  • Gene Conversion / genetics
  • HCT116 Cells
  • Humans
  • Kinetics
  • Multiprotein Complexes / chemistry*
  • Multiprotein Complexes / genetics
  • Poly-ADP-Ribose Binding Proteins / chemistry*
  • Poly-ADP-Ribose Binding Proteins / genetics
  • Topoisomerase II Inhibitors / chemistry
  • Topoisomerase II Inhibitors / pharmacology
  • Torsion, Mechanical
  • Transcription, Genetic
  • Translocation, Genetic / genetics


  • DNA-Binding Proteins
  • Multiprotein Complexes
  • Poly-ADP-Ribose Binding Proteins
  • Topoisomerase II Inhibitors
  • Etoposide
  • DNA
  • DNA Topoisomerases, Type II
  • TOP2A protein, human