Ryuya Fukunaga

Associate Professor


725 N. Wolfe Street
521A Physiology Bldg
Baltimore MD 21205

Biological Chemistry

The Fukunaga lab is broadly interested in RNA biology. More specifically, the Fukunaga lab investigates the mechanism and biology of post-transcriptional gene regulation controlled by small silencing RNAs and RNA-binding proteins. Our research projects will answer fundamental biological questions and also potentially lead to therapeutic applications to human disease.

For the small silencing RNA projects, we are particularly interested in the mechanisms by which the small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced by Dicer enzyme and by which the Dicer enzyme is regulated by Dicer-partner RNA-binding proteins in this small RNA biogenesis functions. Specifically, we aim to understand the molecular mechanism by which the length of small silencing RNAs produced by Dicer is defined and regulated, which is a biologically significant question.

For the RNA-binding proteins projects, we are interested in novel post-transcriptional gene regulation mechanism performed by uncharacterized or poorly characterized RNA-binding proteins. We use Drosophila oogenesis as one of the model systems since post-transcriptional gene regulation is particularly important during oogenesis.

We use a combination of biochemistry, biophysics, Drosophila genetics, cell culture, and next-generation sequencing, in order to understand RNA biology from the atomic to the organismal level.

Zhu L, Fukunaga R. “RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila”. PLoS Genetics. 17(6): e1009655. (2021)

Zhu L, Liao ES, Fukunaga R. “Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodeling during larva-to-adult metamorphosis”. RNA Biology. 16(10):1386-1400. (2019)

Zhu L, Liao ES, Ai Y, Fukunaga R. “RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries”. PLOS ONE. 14(5): e0217603 (2019)

Liao ES, Kandasamy SK, Zhu L, Fukunaga R. “DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner”. RNA. 25: 825-839 (2019)

Zhu L, Kandasamy SK, Liao ES, Fukunaga R. “LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes”. Nature Communications. 9(1):4031 (2018)

Zhu L, Kandasamy SK, Fukunaga R. “Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem”. Nucleic Acid Research. 46, 3726-3741, (2018)

Kandasamy SK, Zhu L, Fukunaga R. “The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2”. RNA, 23, 1139-1153, (2017)

Kandasamy SK, Fukunaga R. “Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production”. Proc. Natl. Acad. Sci. U S A. 113(49):14031-14036, (2016)