University of Fukui reveals cellular memory mechanism

A research group including Professor Masaya Oki of the Department of Applied Chemistry and Biotechnology, Graduate School of Engineering at the University of Fukui, and Graduate Student Takuma Yokosawa at the university's Graduate School of Engineering, announced on June 17 that they have clarified that past experiences of gene expression influence gene expression regulation against future external stimuli, serving as one of the factors that generate differences in responsiveness among cells. Through experiments on budding yeast using a unique single-cell analysis technology, they revealed the existence of an epigenetic expression regulation mechanism where responsiveness decreases due to past expression experiences. This discovery is expected to contribute to clarifying the mechanisms of epigenetic gene expression regulation. The results were published in PNAS Nexus on May 22.

While all cells in any given organism share the same DNA, their genetic responses to external stimuli vary from cell to cell. This heterogeneity is thought to involve epigenetic expression regulation rather than the DNA sequence itself, and disruptions in this process are believed to lead to diseases.

DNA is compactly packaged in the nucleus in the form of heterochromatin, but for a gene to be expressed, this structure must unravel into euchromatin. On the other hand, how these structures change and generate cell-to-cell responsiveness remains poorly understood.

Therefore, the research group aimed to clarify this factor by analyzing gene expression states using budding yeast, a single-celled model organism. The researchers focused on the IMD2 gene in budding yeast, which is expressed in response to the depletion of GTP (guanosine triphosphate). This gene is involved in GTP synthesis and is expressed when GTP is depleted. The stimulus of GTP depletion can be artificially manipulated by adding MPA (mycophenolic acid).

By introducing a fluorescent protein gene to visualize the expression of the IMD2 gene, they confirmed that the expression of IMD2 was induced when the depletion stimulus (MPA) was applied. On the other hand, it became clear that approximately 30% of the cells were repeatedly turning expression on and off even before the depletion stimulus was applied.

To investigate why this difference occurs, the team examined the expression of the IMD2 gene in individual cells over time. As a result, the group of cells that had not experienced expression prior to the MPA stimulation showed a simultaneous rise in expression upon depletion stimulus.

In contrast, the group of cells that had already experienced expression prior to the stimulation did not respond immediately to the depletion stimulus. Furthermore, when they artificially created a euchromatin state by adding NAM (nicotinamide) to force all cells to experience expression, none of the cells responded immediately to the depletion stimulus.

These results revealed that the differences in responsiveness among individual cells to external stimuli depend on past patterns of expression fluctuation. This demonstrates the existence of a "negative memory" in the epigenetic expression regulation mechanism, where responsiveness decreases. This is the opposite of the previously known "positive memory," in which cells that have experienced gene expression once are more likely to express it again.

Oki said, "We believe we have discovered a phenomenon that further expands the concept of cellular memory in epigenetics. Our goal lies in how to apply this to humans. Since each person has different gene expression patterns, we hope that we can predict future states, such as diseases, based on past and present circumstances."

Journal Information
Publication: PNAS Nexus
Title: In the IMD2 gene of Saccharomyces cerevisiae, the expression memory suppresses the induction of expression during guanosine triphosphate depletion
DOI: 10.1093/pnasnexus/pgag179