UChicago scientists are developing a new approach to studying snoRNAs

Dynamic, reversible modifications of DNA and RNA regulate how genes are expressed and transcribed, which can affect cellular processes, disease development, and the overall health of the organism. Small nuclear RNAs (snoRNAs) are a common but neglected group of RNA molecules that direct chemical modifications to cellular ribosomal RNA (rRNA) targets, like an usher showing someone to their seat in a theater.

Researchers from the University of Chicago recently developed a new approach to identify new cellular RNA targets of snoRNAs. They discovered thousands of previously unknown targets for snoRNAs in human cells and mouse brain tissues, including many that serve functions other than directing rRNA modifications. Some of the newly discovered interactions with messenger RNA (mRNA) facilitate protein secretion, an important cellular process that could be exploited for potential therapeutic and biotechnological applications.

Once you see so many targets for these snoRNAs, you realize there is much more to understand. We already see that they play a role in protein secretion, which has important implications for physiology, and suggests a way forward for studying hundreds of other snoRNAs.”

Chuan He, PhD, John T. Wilson Distinguished Service Professor of Chemistry and Professor of Biochemistry and Molecular Biology at the University of Chicago and co-senior author of the paper

The paper, “SnoRNA-facilitated protein secretion found by transcriptome-wide snoRNA target identification,” was published in November 2024 in the journal Cell.

A molecular glue for protein secretion

There are more than 1,000 known genes encoding snoRNAs in the human genome, but scientists have only identified the RNA targets for about 300 of them. These targets mainly include guide modifications for ribosomal RNA and the small nuclear RNA involved in mRNA splicing. In the decades since snoRNAs were first discovered, researchers have largely left the other 700 alone, assuming they performed similar functions. However, unlike other guide RNA molecules such as microRNAs that are all the same length, snoRNAs vary greatly in length from 50-250 residues, suggesting that they can do many different things.

Over the past 12 years, He’s lab has developed various biochemical and sequencing techniques to study transcription, DNA modifications, and RNA modifications. In the new study, he collaborated with co-senior author Tao Pan, PhD, Professor of Biochemistry and Molecular Biology, to test a new tool called “snoKARR-seq” that links snoRNAs to RNAs that bind targets. Bei Liu, PhD, a postdoctoral fellow in Chicago who is co-supervised by He and Pan, led the project.

“Chuan’s lab developed this killing technology to examine exactly which RNA each snoRNA interacts with at the transcriptome level,” Pan said. “Now there is a lot of open space to fully understand what these 1,000 human genes are [that encode snoRNAs] they do”.

Most of the newly discovered snoRNA targets do not overlap with known RNA modification sites, suggesting that snoRNAs may have a much broader function in cells. An unexpected discovery was that it called a snoRNA SNORA73 interacts with mRNAs encoding secreted proteins and cell membrane proteins. Protein secretion is a fundamental biological process by which proteins are transported from a cell to the extracellular space, which is crucial for various functions, including cell-to-cell communication, immune responses, and digestion. The researchers saw it SNORA73 it acts as a “molecular glue” between the mRNA and the protein synthesis machinery that helps facilitate this process.

Further analysis of how SNORA73 binds to mRNA suggests that synthetic snoRNA sequences can be engineered to affect protein secretion. The researchers tested this hypothesis by modifying a green fluorescent protein (GFP) reporter to interact with SNORA73. GFPs are often inserted into cells to make them glow under certain conditions so scientists can see the results of experiments. When the researchers expressed SNORA73 genes with the modified cell-secretable GFP increased protein secretion by 30 to 50% relative to controls.

These experiments showed that they could use the snoRNA machinery to manipulate the secretion of a given protein, which could be useful for developing therapeutics. For example, if a human disease involves a deficiency of secreted proteins, then bioengineers could hack the system to artificially deliver snoRNAs to increase secretion of that protein.

“The field is wide open”

While the technology to synthesize and deliver snoRNA to the right locations is not yet ready, both He and Pan feel confident that these challenges can be solved, building on previous advances in technology using other forms of RNA. They also believe that since snoRNAs are specific to cell types, they could have much more diverse functions—and therapeutic potential—elsewhere.

“Think about neuronal cells, stem cells or cancer cells. There are so many types of cells that one can study. So I think the field is wide open,” he said. “Tao and I have been working together for more than 15 years, and it’s a great showcase of collaboration between the Department of Biological Sciences and the Department of Natural Sciences at UChicago. This work is another example of this kind of collaboration leading to breaking new ground biology.”

Additional authors on the study include Tong Wu, Bernadette A. Miao, Fei Ji, Shun Liu, Pingluan Wang, Yutao Zhao, Yuhao Zhong, Arunkumar Sundaram, Tie-Bo Zeng, Marta Majcherska-Agrawal and Robert J. Keenan of UChicago.