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.

Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology NIH Bethesda MD USA

Genome Damage and Stability Centre University of Sussex Falmer Brighton BN1 9RQ UK

Genome Damage and Stability Centre University of Sussex Falmer Brighton BN1 9RQ UK; Department of Genome Dynamics Institute of Molecular Genetics of the Czech Academy of Sciences 142 20 Prague 4 Czech Republic

Laboratory of Genome Integrity National Cancer Institute NIH Bethesda MD USA

Laboratory of Genome Integrity National Cancer Institute NIH Bethesda MD USA; The Hakubi Center for Advanced Research and Radiation Biology Center Graduate School of Biostudies Kyoto University Kyoto Japan

Research Institute of Molecular Pathology Vienna Biocenter Vienna Austria

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