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The Rigakubu News
The Rigakubu News Sep. 2026
Advancing Science>
~ A Message from a Graduate Student ~
Exploring the Function of Molecular Scissors That Remained Undiscovered for 20 Years
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Mitsunaga Hamashima |
| Department of Biological Sciences, 1st-year Ph.D. student |
| Hometown , Tokyo |
Undergraduate Department: Department of Biological Sciences (Biology), Faculty of Science, Hokkaido University |
When people hear the term “RNA”—which has now become familiar to the general public—many likely think of mRNA, the blueprint for proteins. However, cells contain numerous “non-coding RNAs” that, while they do not become proteins, are essential for various biological processes. Intrigued by their diverse functions, I joined a molecular biology laboratory.
My research focused on the “molecular scissors” necessary for the production of a type of non-coding RNA called snoRNA (Note 1). After snoRNA is transcribed within the cell, its unnecessary parts must be precisely cut away and processed into the correct form before it can perform its intended function.In other words, without these “cutting scissors,” snoRNA cannot be completed. Although this cleavage phenomenon had been known for over 20 years, the specific proteins that function as these “scissors” had remained unidentified for many years.
First, we narrowed down candidate proteins based on data left behind in the lab and confirmed them through experiments to detect RNA. Although it was my first time conducting such an experiment, when the results came out exactly as intended, I felt a definite sense of certainty that “this candidate is definitely the one.”
However, this observation alone does not prove that “that protein directly functions as the scissors.” Even if reducing the levels of that protein within the cell caused abnormalities, we could not rule out the possibility that these were secondary effects mediated by other factors.Does the protein itself actually cleave RNA? Does it bind directly to the target RNA within the cell? And how does the “scissors” recognize the RNA? There was a mountain of questions that needed to be resolved in order to elevate our hypothesis to the status of “fact.”The strength of molecular biology lies in the diverse experimental systems established through years of accumulated research, which allow us to address such questions using multifaceted approaches.
Therefore, I sought clues to solving these problems not only by utilizing the techniques available in our lab but also by incorporating new methods from the latest research papers and seeking collaboration with other laboratories. Of course, the introduction of new techniques requires painstaking experimental optimization and patience.For example, there was an experiment called CLIP-seq(Note 2), which examines the binding regions of proteins and RNA. There were over 100 manual steps alone, and data analysis on a computer was also required.Even when we followed experimental procedures that had succeeded in other labs, it was far from straightforward, and it took half a year to obtain stable data. However, the exhilaration of that moment—when, after all that trial and error, a hypothesis is neatly validated—is the greatest joy of research.
The knowledge we learn in high school and Faculty lectures is nothing more than the “results” that previous researchers have uncovered through repeated, hands-on experimentation. But the moment you step into a lab, you’ll find countless unresolved questions that haven’t yet been written in textbooks.The joy of formulating hypotheses, verifying them through experiments, and uncovering facts one by one with my own hands—this is the very motivation behind my research (Note 3).
Note 1 snoRNA (small nucleolar RNA)
A small non-coding RNA involved in the modification and processing of ribosomal RNA. ↑
Note 2 CLIP-seq
An experimental method for comprehensively analyzing protein-RNA binding sites in living cells. ↑
Note 3 For more details, please look forward to our upcoming publication. ↑
The biosynthesis of snoRNA requires “molecular scissors” (known technically as endonucleases), but their actual nature had not been identified until now.