Headshot of Duncan Clarke
Office Address

420 Washington Avenue SE
Minneapolis, MN 55455
United States


Clarke, Ph.D.

Genetics, Cell Biology and Development

We investigate the regulation of chromosome segregation during cell division: a process that must accurately distribute chromosomes to avoid cancer and birth defects. We focus on DNA Topoisomerase II, an enzyme required for mitosis. Aberrant Topo II activity triggers checkpoint mechanisms that fail in cancer cells. We are investigating if checkpoint gene mutations in cancer cells can be exploited to selectively kill metastatic cells. These crucial mechanisms are interrogated by combining yeast genetics, genome engineering of human cells, and imaging of live cells undergoing cell division.

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Research interests

Our goal is to reveal mechanisms that dictate faithful genome transmission. We utilize yeast genetics and human somatic cell genetics to investigate the mechanics and regulation of mitosis. We primarily focus on DNA Topoisomerase II because impaired Topo II function results in aneuploidy that causes birth defects and cancer. Topo II is also important clinically because it is the target of extensively prescribed anti-cancer drugs. We have sought to understand the biological functions of Topo II in vivo. A major role of Topo II in mitosis is to facilitate condensation of the chromosomes and to permit separation of the sister chromatids in anaphase. An unexpected finding was our identification of the “Decatenation Checkpoint” that responds to perturbed Topo II activity by initiating cell cycle arrest before anaphase. This checkpoint mechanism has since been widely studied in its clinical context, where Topo II is inhibited by cancer drugs. Our recent work has demonstrated that trapped conformational states of Topo II trigger activation of a mitotic cell cycle checkpoint response. We are also investigating the dynamic properties of human Topo II in mitosis, and have revealed that a novel regulatory domain, named the Chromatin Tether (ChT domain), is essential for mitosis and regulates the turn-over dynamics of Topo II on mitotic chromosomes. By revealing the complexities of Topo II function and regulation in mitosis, we will gain insight into causes of aneuploidy and will provide opportunities for improved cancer therapies.

Selected publications

Soliman T, Keifenheim D, Parker PJ & Clarke DJ (2023). Cell Cycle responses to Topoisomerase II inhibition: Molecular Mechanisms and Clinical Implications. The Journal of Cell Biology 222(12): e202209125. doi: 10.1083/jcb.202209125.

Sundararajan S, Park H, Kawano S, Johansson M, Lama B, Saito-Fujita T, Saitoh N, Arnaoutov A, Dasso M, Wang Z, Keifenheim D, Clarke DJ, Azuma Y (2023). Methylated histones on mitotic chromosomes promote topoisomerase IIα function for high fidelity chromosome segregation. iScience, 26(5):106743. doi: 10.1016/j.isci.2023.106743.

Parmar S, Gonzalez SJ, Heckel JM, Mukherjee S, McClellan M, Clarke DJ, Johansson M, Tank D, Geisness A, Wood DK, Gardner MK (2023). Robust microtubule dynamics facilitate low-tension kinetochore detachment in metaphase. The Journal of Cell Biology, 222(8): e202202085. doi: 10.1083/jcb.202202085.

Edgerton HD, Mukherjee S, Johansson M, Bachant J, Gardner MK, Clarke DJ (2023). Low tension recruits the yeast Aurora B protein Ipl1 to centromeres in metaphase. J Cell Sci. 136(16): jcs261416. doi: 10.1242/jcs.261416.

Pandey, N, Keifenheim, D, Yoshida, MM, Hassebroek, V, Soroka, C, Azuma, Y, and Clarke, DJ (2020). Topoisomerase II SUMOylation activates a metaphase checkpoint via Haspin and Aurora B kinases. The Journal of Cell Biology, 219(1): e201807189. doi: 10.1083/jcb.201807189.

Edgerton H, Johansson M, Keifenheim D, Mukherjee S, Chacón JM, Bachant J, Gardner MK and Clarke DJ (2016). A Non-Catalytic Function of the Topoisomerase II CTD in Aurora B Recruitment to Inner Centromeres during Mitosis. Journal of Cell Biology 213(6):651-64.

Chacón JM, Mukherjee S, Schuster BM, Clarke DJ and Gardner MK (2014). Pericentromere tension is self-regulated by spindle structure in metaphase. Journal of Cell Biology, 205(3):313-24.

Lane AB, Giménez-Abián JF and Clarke DJ (2013). A novel Chromatin Tether domain controls topoisomerase IIα dynamics and mitotic chromosome formation. Journal of Cell Biology, 203:471-486.

Furniss K, Tsai H-J, Byl JAW, Lane AB, Vas AC, Hsu WS, Osheroff N and Clarke DJ (2013). Direct monitoring of the strand passage reaction of DNA topoisomerase II triggers checkpoint activation. PLoS Genetics, 9(10): e1003832.

Hsu WS, Erickson SL, Tsai HJ, Andrews CA, Vas ACJ and Clarke DJ (2011). S-phase cyclin-dependent kinases promote sister chromatid cohesion in budding yeast. Molecular & Cellular Biology, 31(12):2470-83.

Vas ACJ, Andrews CA, Kirkland-Matesky K and Clarke DJ (2007). In vivo analysis of chromosome condensation in Saccharomyces cerevisiae. Molecular Biology of the Cell, 18(2):557-568.

Andrews CA, Vas ACJ, Meier B, Giménez-Abián JF, Díaz-Martínez LA, VanderWaal K, Hsu W-S, Erickson S and Clarke DJ (2006). A Mitotic Topoisomerase II Checkpoint in Budding Yeast is required for Genome Stability but acts independently of Pds1/Securin. Genes & Development, 20:1162-1174.