Every day, the human body replaces an estimated 300 billion cells through mitosis, the process in which a single cell divides into two identical daughter cells. As though the sheer number of cell divisions wasn’t staggering enough, the molecular machinery that enables the feat is even more remarkable, resembling an exceedingly efficient factory within each dividing cell. At the center of the factory, keeping the strands of DNA from becoming hopelessly tangled, is a specialized protein called topoisomerase II, or Topo II for short.
“It’s a really ancient enzyme and must have coevolved with DNA,” explains Duncan Clarke, a professor in the Department of Genetics, Cell Biology, and Development. Without Topo II, he notes, cells would be unable to complete replication or divide properly, making the protein essential for all living organisms, not just humans. For more than three decades, Clarke has focused much of his research on understanding how this enzyme works.
Before mitosis, during the DNA replication phase of the cell cycle, the helix is unwound and separated into two strands. As the strands are pulled apart, the helix winds back on itself. If the coiling went unchecked, the DNA would be unable to separate. Topo II solves the problem by grabbing two entangled segments of the DNA helix, breaking both strands of one segment, passing the other through the gap, and then repairing the break—like snipping a loop of yarn to untangle a knot and then seamlessly mending it. The enzyme plays a similar role during mitosis, when the duplicated chromosomes must be disentangled from one another before they can be pulled into the new cells.
Clarke’s research as a graduate student at the University of Cambridge in the early 1990s helped uncover that Topo II also functions as a molecular checkpoint. If the enzyme is inhibited, cell division grinds to a stop. The results were published in Nature. “Back then, we didn’t really have much of a molecular understanding of how this worked,” Clarke explains. “It was more of a description of what cells do.” Clarke has since helped define how cells monitor Topo II activity, identifying key proteins and signaling pathways involved at two distinct stages where cell division can be halted.
These Topo II checkpoints are essential because even one lingering knot can lead to catastrophic errors during cell division, causing genetic disorders and developmental abnormalities. Given the critical role Topo II plays in cell division, it has also become a key target for chemotherapy drugs, which disrupt the enzyme to prevent cancerous cells from multiplying.
Building on this understanding, Clarke’s lab has turned to the intricate details of how Topo II functions. In recent years, they discovered a small segment of the enzyme that acts as an internal guidance system, steering Topo II toward specific regions of the chromosome. Their research suggests this segment—known as the chromatin tether—is remarkably precise: It appears to recognize particular chemical markers on the chromosome, including a marker strongly associated with certain forms of cancer. The finding has sparked new collaborations with medical researchers and could open promising avenues for targeted treatment strategies.
The more Clarke learns about the machinery of cell division, the more rewarding the research becomes. In collaboration with longtime colleague Yoshiaki Azuma, a biochemist at the University of Kansas, his lab is now investigating another protein that partners with Topo II during mitosis. This protein, known as PICH, is often overproduced in certain cancers, making it a compelling focus for drug development. Clarke and Azuma have begun screening for chemical compounds that inhibit PICH’s activity, and early results are encouraging. “It’s always the next thing that’s most exciting,” Clarke says. “That’s what keeps you going.” — Jonathan Damery