Researchers at Penn State have discovered that two proteins within a cellular complex can have opposing effects on the stability of messenger RNA (mRNA) in human cells. The study, conducted using human colorectal cancer cells, may help explain how various diseases, such as cancers and neurodegenerative disorders, develop and could inform new treatment approaches.
The focus of the research was on the CCR4-NOT protein complex, which is responsible for removing mRNA after it has delivered genetic instructions needed to make proteins. Previously, scientists believed that all proteins within this complex worked together. However, the Penn State team found that one protein destabilizes mRNA while another stabilizes it.
"Traditionally, subunits are expected to work together toward a common function, but our results show that CNOT4 has unique roles beyond RNA degradation or catalysis," said Shardul Kulkarni, assistant research professor of biochemistry and molecular biology at Penn State and first author of the study. "Our study shows that not all subunits of a 'degradation' complex act the same way - some can have distinct and even opposing roles. Understanding these opposing forces gives us a clearer picture of how cells maintain balanced gene expression and could point to new ways to intervene when that balance is lost."
Kulkarni compared gene regulation to adjusting a dimmer switch: "The study of gene regulation is essential for understanding cellular differentiation, the progression from a single embryonic cell to a multicellular organism, and the mechanisms by which organisms adapt to environmental stimuli," he said. He explained that disruptions in this regulatory system can lead to diseases such as cancer or metabolic problems.
The team used an experimental tool called the auxin-inducible degron (AID) system, which allows scientists to rapidly turn off specific proteins in human cells by tagging them for destruction. This method enabled precise observation of what happens when either CNOT1 or CNOT4 was removed from colorectal cancer cells.
With this approach, they observed that depleting CNOT1 slowed down mRNA decay and altered thousands of RNA transcripts. In contrast, removing CNOT4 promoted faster mRNA degradation but had less effect on transcript variety.
"Understanding the intricacies of the opposing effects CNOT1 and CNOT4 have on mRNA stability has several implications," Kulkarni said. He noted that these findings could aid in identifying disease situations where these proteins are out of balance and could help develop new biomarkers or therapies targeting mRNA stability.
Other contributors included graduate students Courtney Smith and Oluwasegun T. Akinniyi; Belinda M. Giardine; Cheryl A. Keller; and Alexei Arnaoutov from NIH's National Institute of Child Health and Human Development.
This research relied on core facilities managed by Penn State’s Huck Institutes of the Life Sciences—specifically proteomics, genomics, flow cytometry facilities—and received funding from the National Institutes of Health.
