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Ryuya Fukunaga on Small Silencing RNAs

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Ryuya Fukunaga on Small Silencing RNAs

Interviewed by Catherine Gara

Ryuya Fukunaga on Small Silencing RNAs

Ryuya Fukunaga is an assistant professor of biological chemistry. He studies small RNA molecules that help control which proteins get made and when.

Q: What does your laboratory study?

FUKUNAGA: We work on noncoding RNA. RNA used to be thought of as just an intermediate molecule that transfers protein coding information from DNA to ribosomes, where proteins are made. That’s messenger, or mRNA. In the last two decades, we have learned that there are many types of RNA: Some interact with DNA to increase or decrease gene activity, some interact with mRNA to prevent proteins from being made and others can even work as enzymes to catalyze reactions.

Q: What types of noncoding RNA are you most interested in?

FUKUNAGA: We are trying to understand a group called small silencing RNAs. We want to know how they are produced in cells and how they function.

There are two main kinds that we know of: microRNA (miRNA) and small interfering RNA (siRNA), both discovered in the 1990s. Both are short (20 to 25 “letters” long) and linear, and they bind to mRNA in a targeted way, when their “letter” sequences match.

When an miRNA binds to an mRNA, it temporarily prevents that mRNA from being used as a blueprint for protein. There are more than 2,000 miRNA genes in the human genome, and we know that mutations in at least some of those genes are direct causes of diseases like deafness, cancer and cardiovascular disease.

When siRNAs bind to mRNA, they signal for the mRNA to get chopped up by an enzyme so that it never gets used to make protein. They’re often used to disable viral RNA.

Q: What kind of experiments do you do?

FUKUNAGA: We do a lot of fruit fly genetics and high-throughput sequencing. If we suspect that a particular gene is important for producing small silencing RNAs, we might delete that gene in fruit flies, see if any abnormalities result, and then sequence their RNA and compare it to the RNA of normal flies to see if any small silencing RNAs were affected. With high-throughput sequencing technology, you can measure the levels of hundreds of thousands of RNA molecules in a single experiment. We also perform biochemical experiments to figure out how molecules are interacting to produce the results we see.

Fukunaga on top of Mt. Fuji Fukunaga, in 2013, on top of Mt. Fuji, the tallest mountain in Japan at 12,388 ft.

Q: What drew you to science?

FUKUNAGA: As I child, I was always interested in the mechanism behind what I observed, and that’s what science is. I wanted to know about myself: What are we? How do we exist, survive and think?

Q: What do you enjoy doing in your free time?

FUKUNAGA: Mostly jogging. I also did some mountain climbing back in Japan, and when I was in California for a postdoc, I visited a lot of national parks, like Yosemite and the Grand Canyon.