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

Andres Canela, Yaakov Maman, Shar yin N. Huang, Gordana Wutz, Wen Tang, Guido Zagnoli-Vieira, Elsa Callen, Nancy Wong, Amanda Day, Jan Michael Peters, Keith W. Caldecott, Yves Pommier, André Nussenzweig

Research output: Contribution to journalArticlepeer-review

117 Scopus citations


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.

Original languageEnglish
Pages (from-to)252-266.e8
JournalMolecular Cell
Issue number2
StatePublished - 25 Jul 2019
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2019


We thank Sam John for comments on the manuscript; Barry Sleckman for the pre-B cell lines and Masato Kanemaki for HCT116 RAD21-mAID cells; Fred Alt for discussions; Yoram Louzoun for advice on quantitative modeling; Jennifer Wise and Kelly Smith for assistance with animal work; Xuguang Tai for assistance on primary lymphocytes isolation; and David Goldstein and the CCR Genomics core for sequencing support. Y.P. and S.N.H. are supported by the Intramural Program of the NIH , Center for Cancer Research ( Z01 BC006161 ). Research in the laboratory of J.-M.P. is funded by Boehringer Ingelheim and grants by the Austrian Research Promotion Agency ( FFG - 834223FFG - 852936 ) and the European Research Council H2020 ( 693949 ). A.C. is in part supported by the Kyoto University Hakubi Project. The A.N. laboratory is supported by the Intramural Research Program of the NIH , an Ellison Medical Foundation Senior Scholar in Aging Award ( AG-SS-2633-11 ), the Department of Defense Idea Expansion ( W81XWH-15-2-006 ) and Breakthrough ( W81XWH-16-1-599 ) Awards, the Alex Lemonade Stand Foundation Award, and an NIH Intramural FLEX Award.

FundersFunder number
Center for Cancer ResearchZ01 BC006161
Department of Defense Idea ExpansionW81XWH-15-2-006, W81XWH-16-1-599
National Institutes of Health
National Cancer InstituteZIABC010959
Ellison Medical FoundationAG-SS-2633-11
Boehringer Ingelheim
Alex's Lemonade Stand Foundation for Childhood Cancer
H2020 European Research Council693949
Österreichische Forschungsförderungsgesellschaft834223FFG - 852936
Kyoto University


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


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