Genes Can Respond to Coded Information in Signals

This is a modified version of an article written by Matt Shipman, Research Lead in University Communications.

Professor Albert Keung and his colleagues have demonstrated that genes are capable of responding to coded information in light signals in predictable ways, as well as filtering out some signals entirely. The study shows how a single mechanism can trigger different behaviors from the same gene – and has applications in the biotechnology sector.

“The fundamental idea here is that you can encode information in the dynamics of a signal that a gene is receiving,” says Prof. Keung, corresponding author of a paper on the work. “So, rather than a signal simply being present or absent, the way in which the signal is being presented matters.”

For this study, the researchers modified a yeast cell so that it has a gene that produces fluorescent proteins when the cell is exposed to blue light.

Here’s how that works. A region of the gene called the promoter is responsible for controlling the gene’s activity. In the modified yeast cells, a specific protein is attached to the promoter region of the gene. When researchers shine blue light on that protein, it becomes capable of binding with a second protein. When the second protein binds to the first protein, the gene becomes active. And that’s easy to detect, since the activated gene produces proteins that glow in the dark.

The researchers then exposed these yeast cells to 119 different light patterns. Each light pattern differed in terms of the intensity of the light, how long each pulse of light was, and how frequently the pulses occurred. The researchers then mapped out the amount of fluorescent protein that the cells produced in response to each light pattern.

People talk about genes being turned on or off, but in this case it’s less like a light switch and more like a dimmer switch – a gene can be activated a little bit, a lot, or anywhere in between. If a given light pattern leads to the production of a lot of fluorescent protein, that means the light pattern made the gene very active. If the light pattern led to the production of just a small amount of fluorescent protein, that means the pattern only triggered mild activity of the gene.

“We found that different light patterns can produce very different outcomes in terms of gene activity,” says Jessica Lee, first author of the paper and a recent Ph.D. graduate from Prof. Keung’s research group. “The big surprise, to us, was that the output was not directly correlated to the input. Our expectation was that the stronger the signal, the more active the gene would be. But that wasn’t necessarily the case. One light pattern might make the gene significantly more active than another light pattern, even if both patterns were exposing the gene to the same amount of light.”

The researchers found that all three light pattern variables – intensity of the light, frequency of the light pulses, and how long each pulse lasted – could influence gene activity, but found that controlling the frequency of light pulses gave them the most precise control over gene activity.

“We also used the experimental data to develop a computational model that helped us better understand why different patterns produce different levels of gene activity,” says Leandra Caywood, co-author of the paper and a current Ph.D. student in the Keung Research Group.

“For example, we found that when you spread rapid pulses of light far enough apart, you get more gene activity than you would expect from the amount of light being applied,” Caywood says. “Using the model, we were able to determine that this is happening because the proteins can’t separate and come back together quickly enough to respond to every pulse when they are bunched up. Basically, the proteins don’t have time to fully separate from each other between pulses, so are spending more time connected – meaning that the gene is spending more time activated even when the light is off. Understanding these sorts of dynamics is very useful for helping us figure out how to better control gene activity using these signals.”

“Our finding is relevant for cells that respond to light, such as those found in leaves,” Keung says. “But it also tells us that genes are responsive to signal patterns, which could be delivered by mechanisms other than light, such as a chemical signal.”

The researchers say this work enables future studies that advance our understanding of the dynamics of cell behavior and gene expression.

In the nearer term, the researchers say there are practical applications for the work in the pharmaceutical and biotech sectors.

“In biomanufacturing, you often want to manage both the growth of cells and the rate at which those cells are producing specific proteins,” Lee says. “Our work here can help manufacturers fine-tune and control both of those variables.”

The paper, “Mapping the Dynamic Transfer Functions of Eukaryotic Gene Regulation,” is published in the journal Cell Systems. The paper was co-authored by Jennifer Lo and Nicholas Levering, who were both undergraduates at NC State when the work was done.

The work was done with support from the National Science Foundation, under Emerging Frontiers in Research and Innovation grant 1830910; and from the National Institutes of Health, under grant 5T32GM133366.