About

Duncan Clarke, PhD, is a professor at the University of Minnesota Medical School, with a research focus on mechanisms that dictate faithful genome transmission. His work utilizes yeast genetics and human somatic cell genetics to investigate the mechanics and regulation of mitosis, with a primary focus on DNA Topoisomerase II (Topo II). Impaired Topo II function results in aneuploidy, which causes birth defects and cancer, making it a significant target in clinical treatments. Clarke's research aims to understand the biological functions of Topo II in vivo, particularly its role in facilitating chromosome condensation and sister chromatid separation during mitosis. A notable contribution from his lab is the identification of the 'Decatenation Checkpoint,' a mechanism that responds to perturbed Topo II activity by initiating cell cycle arrest before anaphase. His recent work has demonstrated that aberrant conformational states of Topo II trigger activation of this mitotic checkpoint. Additionally, Clarke's team investigates the dynamic properties of human Topo II in mitosis, revealing that a regulatory domain called the Chromatin Tether (ChT domain) is essential for proper mitotic function. Without proper regulation of Topo II turnover on mitotic chromosomes, chromosome condensation fails, leading to aberrant mitosis. Through revealing the complexities of Topo II function and regulation, Clarke's research provides insights into the causes of aneuploidy and offers opportunities for improved cancer therapies.

Research topics

• Biology
• Cell biology
• Genetics
• Molecular biology
• Biochemistry
• Chemistry

Selected publications

• PICH impacts the spindle assembly checkpoint via its DNA translocase and SUMO-interaction activities

  Life Science Alliance · 2025-02-07

  articleOpen access

  Either inhibiting or stabilizing SUMOylation in mitosis causes defects in chromosome segregation, suggesting that dynamic mitotic SUMOylation of proteins is critical to maintain integrity of the genome. Polo-like kinase 1–interacting checkpoint helicase (PICH), a mitotic chromatin remodeling enzyme, interacts with SUMOylated chromosomal proteins via three S UMO- i nteracting m otifs (SIMs) to control their association with chromosomes. Using cell lines with conditional PICH depletion/PICH replacement, we revealed mitotic defects associated with compromised PICH functions toward SUMOylated chromosomal proteins. Defects in either remodeling activity or SIMs of PICH delayed mitotic progression caused by activation of the spindle assembly checkpoint (SAC) indicated by extended duration of Mad1 foci at centromeres. Proteomics analysis of chromosomal SUMOylated proteins whose abundance is controlled by PICH activity identified candidate proteins to explain the SAC activation phenotype. Among the identified candidates, Bub1 kinetochore abundance is increased upon loss of PICH. Our results demonstrated a novel relationship between PICH and the SAC, where PICH directly or indirectly affects Bub1 association at the kinetochore and impacts SAC activity to control mitosis.

  PublisherOA PDFDOI

• Histone H3 N-Terminal Tail Residues Important for Meiosis in Saccharomyces cerevisiae

  Biomolecules · 2025-08-21

  articleOpen accessSenior authorCorresponding

  Histone tail phosphorylation has diverse effects on a myriad of cellular processes, including cell division, and is highly conserved throughout eukaryotes. Histone H3 phosphorylation at threonine 3 (H3T3) during mitosis occurs at the inner centromeres and is required for proper biorientation of chromosomes on the mitotic spindle. While H3T3 is also phosphorylated during meiosis, a possible role for this modification has not been tested. Here, we asked if H3T3 phosphorylation is important for meiotic division by quantifying sporulation efficiency and spore viability in Saccharomyces cerevisiae mutants with a T3A amino acid substitution. The T3A substitution resulted in reduced sporulation efficiency and reduced spore viability. Analysis of two other H3 tail mutants, K4A and S10A, revealed different effects on sporulation efficiency and spore viability compared to the T3A mutant, suggesting that these phenotypes may be due to failures in distinct functions. To determine if the spindle checkpoint promotes spore viability of the T3A mutant, the MAD2 gene was deleted. This resulted in a severe reduction in spore viability following meiosis. Altogether, the data reveal an important function for histone H3 threonine 3 that requires monitoring by the spindle checkpoint to ensure successful completion of meiosis.

  PublisherOA PDFDOI

• Histone H3 tail modifications required for meiosis in <i>Saccharomyces cerevisiae</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-11

  preprintOpen accessSenior authorCorresponding

  Abstract Histone tail phosphorylation has diverse effects on a myriad of cellular processes, including cell division, and is highly conserved throughout eukaryotes. Histone H3 phosphorylation at threonine 3 (H3T3) during mitosis occurs at the inner centromeres and is required for proper biorientation of chromosomes on the mitotic spindle. While H3T3 is also phosphorylated during meiosis, a possible role for this modification has not been tested. Here, we asked if H3T3 phosphorylation (H3T3ph) is important for meiotic division by quantifying sporulation efficiency and spore viability in Saccharomyces cerevisiae mutants with a T3A amino acid substitution. The T3A substitution resulted in greatly reduced sporulation efficiency and reduced spore viability. Analysis of two other H3 tail mutants, K4A and S10A, revealed different effects on sporulation efficiency and spore viability compared to the T3A mutant, suggesting that these phenotypes are due to failures in distinct functions. To determine if the spindle checkpoint promotes spore viability of the T3A mutant, the MAD2 gene required for the spindle assembly checkpoint was deleted to abolish spindle assembly checkpoint function. This resulted in a severe reduction in spore viability following meiosis. Altogether, the data reveal a critical function for histone H3 threonine 3 that requires monitoring by the spindle checkpoint to ensure successful completion of meiosis.

  PublisherOA PDFDOI

• Robust microtubule dynamics facilitate low-tension kinetochore detachment in metaphase

  The Journal of Cell Biology · 2023 · 9 citations

  • Cell biology
  • Biology
  • Genetics

  During mitosis, sister chromatids are stretched apart at their centromeres via their attachment to oppositely oriented kinetochore microtubules. This stretching generates inwardly directed tension across the separated sister centromeres. The cell leverages this tension signal to detect and then correct potential errors in chromosome segregation, via a mechanical tension signaling pathway that detaches improperly attached kinetochores from their microtubules. However, the sequence of events leading up to these detachment events remains unknown. In this study, we used microfluidics to sustain and observe low-tension budding yeast metaphase spindles over multiple hours, allowing us to elucidate the tension history prior to a detachment event. We found that, under conditions in which kinetochore phosphorylation weakens low-tension kinetochore-microtubule connections, the mechanical forces produced via the dynamic growth and shortening of microtubules is required to efficiently facilitate detachment events. Our findings underscore the critical role of robust kinetochore microtubule dynamics in ensuring the fidelity of chromosome segregation during mitosis.

  PublisherOA PDFDOI

• Methylated histones on mitotic chromosomes promote topoisomerase IIα function for high fidelity chromosome segregation

  iScience · 2023 · 11 citations

  • Biology
  • Cell biology
  • Genetics

  . Here, we present evidence that the Chromatin Tether (ChT) within the CTD interacts with specific methylated nucleosomes and is crucial for high-fidelity chromosome segregation. Mutation of individual αChT residues disrupts αChT-nucleosome interaction, induces loss of segregation fidelity and reduces association of TopoIIα with chromosomes. Specific methyltransferase inhibitors reducing histone H3 or H4 methylation decreased TopoIIα at centromeres and increased segregation errors. Methyltransferase inhibition did not further increase aberrant anaphases in the ChT mutants, indicating a functional connection. The evidence reveals novel cellular regulation whereby TopoIIα specifically interacts with methylated nucleosomes via the αChT to ensure high-fidelity chromosome segregation.

  PublisherOA PDFDOI

• Cell cycle responses to Topoisomerase II inhibition: Molecular mechanisms and clinical implications

  The Journal of Cell Biology · 2023-11-13 · 25 citations

  reviewOpen accessSenior authorCorresponding

  DNA Topoisomerase IIA (Topo IIA) is an enzyme that alters the topological state of DNA and is essential for the separation of replicated sister chromatids and the integrity of cell division. Topo IIA dysfunction activates cell cycle checkpoints, resulting in arrest in either the G2-phase or metaphase of mitosis, ultimately triggering the abscission checkpoint if non-disjunction persists. These events, which directly or indirectly monitor the activity of Topo IIA, have become of major interest as many cancers have deficiencies in Topoisomerase checkpoints, leading to genome instability. Recent studies into how cells sense Topo IIA dysfunction and respond by regulating cell cycle progression demonstrate that the Topo IIA G2 checkpoint is distinct from the G2-DNA damage checkpoint. Likewise, in mitosis, the metaphase Topo IIA checkpoint is separate from the spindle assembly checkpoint. Here, we integrate mechanistic knowledge of Topo IIA checkpoints with the current understanding of how cells regulate progression through the cell cycle to accomplish faithful genome transmission and discuss the opportunities this offers for therapy.

  PublisherOA PDFDOI

• Low tension recruits the yeast Aurora B protein Ipl1 to centromeres in metaphase

  Journal of Cell Science · 2023-07-31 · 6 citations

  articleOpen accessSenior author

  Accurate genome segregation in mitosis requires that all chromosomes are bioriented on the spindle. Cells monitor biorientation by sensing tension across sister centromeres. Chromosomes that are not bioriented have low centromere tension, which allows Aurora B (yeast Ipl1) to perform error correction that locally loosens kinetochore-microtubule attachments to allow detachment of microtubules and fresh attempts at achieving biorientation. However, it is not known whether low tension recruits Aurora B to centromeres or, alternatively, whether low tension directly activates Aurora B already localized at centromeres. In this work, we experimentally induced low tension in metaphase Saccharomyces cerevisiae yeast cells, then monitored Ipl1 localization. We find low tension recruits Ipl1 to centromeres. Furthermore, low tension-induced Ipl1 recruitment depended on Bub1, which is known to provide a binding site for Ipl1. In contrast, Top2, which can also recruit Ipl1 to centromeres, was not required. Our results demonstrate cells are sensitive to low tension at centromeres and respond by actively recruiting Ip1l for error correction.

  PublisherOA PDFDOI

• Cell cycle checkpoints and cell surface damage

  BioEssays · 2022-04-27

  letterSenior authorCorresponding

  Data sharing is not applicable to this article as no new data were created or analyzed in this study.

  PublisherDOI

• Role of Aurora B and Haspin kinases in the metaphase Topoisomerase II checkpoint

  Cell Cycle · 2021 · 8 citations

  Senior authorCorresponding
  • Biology
  • Cell biology
  • Molecular biology

  DNA Topoisomerase II (TopoII) uses ATP hydrolysis to decatenate chromosomes so that sister chromatids can faithfully segregate in mitosis. When the TopoII enzyme cycle stalls due to failed ATP hydrolysis, the onset of anaphase is delayed, presumably to allow extra time for decatenation to be completed. Recent evidence revealed that, unlike the spindle assembly checkpoint, this TopoII checkpoint response requires Aurora B and Haspin kinases and is triggered by SUMOylation of the C-terminal domain of TopoII.

  PublisherOA PDFDOI

• Role of the Topoisomerase IIα Chromatin Tether domain in Nucleosome Binding &amp; Chromosome Segregation

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-10-03

  preprintOpen accessCorresponding

  Abstract Due to the intrinsic nature of DNA replication, replicated genomes retain catenated genomic loci that must be resolved to ensure faithful segregation of sister chromatids in mitosis. Type II DNA Topoisomerase (TopoII) decatenates the catenated genomic DNA through its unique Strand Passage Reaction (SPR). Loss of SPR activity results in anaphase chromosome bridges and formation of P olo-like Kinase I nteracting C heckpoint H elicase (PICH)-coated ultra-fine DNA bridges (UFBs) whose timely resolution is required to prevent micronuclei formation. Vertebrates have two TopoII isoforms– TopoIIα and TopoIIβ, that share a conserved catalytic core. However, the essential mitotic function of TopoIIα cannot be compensated by TopoIIβ, due to differences in their catalytically inert C-terminal domains (CTDs). Using genome-edited human cells, we show that specific binding of TopoIIα to methylated histone, tri-methylated H3K27 (H3K27me3), via its Chromatin Tether (ChT) domain within the CTD contributes critically to avoid anaphase UFB formation. Reducing H3K27 methylation prior to mitosis increases UFBs, revealing a requirement for proper establishment of H3K27me3 after DNA replication to facilitate TopoIIα-ChT dependent UFB prevention. We propose that interaction of the TopoIIα-ChT with H3K27me3 is a key factor that ensures the complete resolution of catenated loci to permit faithful chromosome segregation in human cells. Summary Statement Genomic catenations originating from the DNA replication process must be resolved by DNA Topoisomerase II (TopoII) to permit sister chromatid disjunction. The results show that specific recognition of methylated histone containing chromatin by TopoII is critical for complete resolution of the genome.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R21CA095914

  NIH · $297k · 2004

• NIH Grant R01CA099033

  NIH · $1.6M · 2009

• Regulation of kinetochore function by Topoisomerase II

  NIH · $1.2M · 2015–2019

• Chromosome Condensation in Yeast

  NSF · $540k · 2009–2012

• Control of Chromosome Segregation by DNA Topoisomerase II

  NIH · $2.2M · 2019–2028

Frequent coauthors

• Juan F. Giménez-Abián

  Centro de Investigaciones Biológicas Margarita Salas

  48 shared

• Laura A. Díaz-Martínez

  Gonzaga University

  25 shared

• C. Stephen Downes

  University of Ulster

  17 shared

• Robert T. Johnson

  15 shared

• Steven I. Reed

  14 shared

• Marisa Segal

  University of Cambridge

  14 shared

• G. Giménez‐Martín

  Consejo Superior de Investigaciones Científicas

  11 shared

• Catherine A. Andrews

  AgResearch

  10 shared

Awards & honors

• Dr. James E. Rubin Medical Memorial Award
• Graduating Medical Student Research Award
• Veneziale-Steer Award
• Dr. Marvin and Hadassah Bacaner Research Awards
• Schmidt Steer Award