The Human Genome Project was launched in 1990, preceded by decades of breakthroughs in genetics. It eventually gave us a sequence of the human genome.
Yet, while the physical rules behind the genome's organization remain an active area of research, many questions are still largely unanswered. Among these is the impact of an omnipresent force influencing life on Earth: gravity.
A new study, which appears in the journal Science Advances, addresses some of these weighty questions by using an innovative technique: creating a zero-gravity, or microgravity, environment in order to reveal gravity's impact on a human cell.
The method serves two purposes: isolating gravity's impact on the genome by removing it as a factor in experiments while, at the same time, showing how the genome functions in outer space, where gravity is nonexistent.
"On Earth, the role of gravity is intriguing—it is a constant mechanical stress on everything," explains Alexandra Zidovska, an associate professor in New York University's Department of Physics, who led the study. "We wanted to know what gravity's role is in the genome's organization and function here on Earth. To uncover it, you have to remove gravity as a force so we simulated zero gravity in our experiments."
"Beyond Earth, the question of lack of gravity is also compelling: How will the human genome be affected when in outer space?" she continues. "We think our findings can be useful in better understanding how space travel affects us."
The human genome has a complex and compact hierarchical organization. It is a one-dimensional sequence encoded in two meters of DNA molecules packed in three dimensions inside a cell nucleus barely 10 micrometers in size—or about the width of a silk fiber.
Its structure is directly linked to its function, and deviations from it can lead to human diseases, such as cancer, and developmental afflictions. Despite their significance, physical principles governing the genome's organization are not well understood.
"We do not know if or how the presence of gravity affects this organization and if the absence of gravity would cause genomic aberrations," observes Zidovska.
To explore this question, the NYU researchers designed and built a custom-tailored laboratory device, a random positioning machine that allows for imaging of the human genome in live cells. In addition, they prepared dishes of live cells that were free of air bubbles, which can interfere with measurements. The machine then rotated these dishes along two independent axes, following a 3D rotational path that leads to a simulated microgravity—or weightlessness on Earth. It is akin to the larger devices astronauts use in their training.
In addition, the researchers developed novel 3D rotational algorithms, which not only simulated microgravity, but minimized the generation of fluid flows, which are normally generated during a 3D rotation but are nonexistent in zero gravity conditions outside Earth.
Moreover, they also created algorithms to investigate the effects of flows on the cells and the genome. Together, these technological advances led to a reduction of both flows and the formation of cell aggregates, which were often obscuring the effects of simulated microgravity in previous studies.
To shed light on the effects of simulated microgravity and flows on the cell and the cell nucleus, the researchers compared cells exposed to simulated microgravity with minimized flows, with cells exposed to strong flows—as well as cells with no exposure at all.
After exposing cells to either simulated microgravity or flows for 24 hours, the scientists used sophisticated imaging techniques to capture cells under these conditions. They then recorded streams of images, which they used to conduct a detailed physical analysis of the cells: changes in the cell shape and volume, the nuclear shape and volume, the nuclear envelope, the genome, and the nucleolus—the largest liquid condensate in the nucleus. More specifically, the researchers investigated changes in the genome's organization, dynamics, and possible DNA damage induced by simulated microgravity.
Overall, the results showed the following:
- The cells' shape became elongated when exposed to flows, but remained unchanged when exposed to simulated microgravity. The volume of the cell nucleus increased after exposure to zero gravity, indicating gravity diminishes it.
- Despite the changes to the nucleus's shape and volume under zero gravity, the thickness and structure of the nuclear envelope remained unchanged, suggesting gravity has minimal impact on these traits.
- The genome inside the cell nucleus maintained its physiological organization and motions after 24-hour exposure.
- The researchers showed that simulated microgravity does not cause DNA damage; however, DNA damage occurs when cells are exposed to flows.
- The nucleolus becomes smoother after exposure to simulated microgravity or flows.
- Overall, a day-long exposure of the nucleus to simulated microgravity led to rather subtle changes, which, the researchers add, could amplify over time and then affect cell physiology.
"Our data show that the genome, its organization, and dynamics are incredibly robust and seem unaffected by gravity, or lack thereof, after 24 hours," observes Zidovska. "In the same way, these results suggest that the physical organization of the human genome may undergo minimal changes in outer space during comparable times. However, such changes could occur during longer exposures and due to DNA damage occurring in space."
The paper's other authors included Nikitas Kanellakopoulos, an NYU doctoral student; NYU undergraduate students Manav Patel, Brandon Sato, and Melaina Lawrence; and Leif Ristroph, an associate professor at NYU's Courant Institute School of Mathematics, Computing, and Data Science.
This research was supported in part by grants from the National Science Foundation (CAREER PHY-1554880, PHY-2210541, CMMI-1762506, NYU MRSEC DMR-1420073) and the National Institutes of Health (R01-GM145924). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
