Bio

Kotaro Nakanishi received his B.S. degree from Tokyo University of Science in 2000, where he studied the allosteric regulation of lactate dehydrogenase. He earned his M.S. degree from the University of Tokyo in 2003, investigating the substrate recognition mechanism of the arginine tRNA–specific ribonuclease colicin D. After several years in industry, he returned to academia and obtained his D.Sc. in 2007 from Tokyo Institute of Technology, where he used X-ray crystallography and biochemistry to study aminoacyl-tRNA synthetases and tRNA modification enzymes under the supervision of Dr. Osamu Nureki. In 2008, Dr. Nakanishi joined the laboratory of Dr. Dinshaw Patel at Memorial Sloan Kettering Cancer Center, where he determined the crystal structures of the Argonaute and Dicer proteins and established the structural principles underlying RNA-guided gene silencing. His work was recognized by several honors, including fellowships from the Japan Society for the Promotion of Science (Young Scientist and Research Abroad), the Human Frontier Science Program Long-Term Fellowship, the RNA Society/Scaringe Award (2012), and the Young Scientists’ Prize of the Commendation for Science and Technology from the Japanese Ministry of Education, Culture, Sports, Science and Technology (2013). Dr. Nakanishi joined The Ohio State University in August 2013. He received the Ohio State Early Career Innovator of the Year in 2024, the Science Coalition Sparking American Economic Growth in 2024, and the Innovators in Healthcare and Life Sciences Award in 2025. He co-founded City Therapeutics in 2023 and has served on its scientific advisory board.

Research Overview

Small noncoding RNAs, including microRNAs (miRNAs) and related RNA species, regulate gene expression by guiding Argonaute (AGO) proteins to complementary target RNAs in a process known as RNA interference (RNAi). In humans, more than 2,000 miRNAs are selectively loaded into four AGO paralogs (AGO1–4) to assemble RNA-induced silencing complexes (RISCs), which repress translation or induce RNA silencing. Dysregulation of this pathway is linked to diverse diseases, including neurodevelopmental disorders and cancer. Although human AGO paralogs were long thought to function redundantly, emerging evidence demonstrates that they have distinct biochemical activities and biological roles. Research in the Nakanishi laboratory focuses on understanding how RNA sequence, length, and structure determine AGO selection, RISC assembly, and downstream gene-silencing outcomes. In particular, the lab has shown that AGO3—previously considered catalytically inactive—can function as a slicer when loaded with specific short guide RNAs, termed cleavage-inducing tiny RNAs (cityRNAs). Our current research directions include: 1. Molecular mechanisms of RISC assembly and maturation, 2. Functional specialization among human AGO paralogs, 3. Regulation of AGO activity by target RNAs and accessory proteins, 4. Structural basis of RNA length control and guide–target recognition, and 5. Engineering cityRNAs for therapeutic and biotechnological applications. To address these questions, the laboratory employs a

multidisciplinary approach combining cryo-electron microscopy, X-ray crystallography, biochemistry, biophysics, molecular and cell biology, and confocal imaging. Beyond fundamental RNA biology, the lab is also interested in translating mechanistic insights into programmable RNA-targeting platforms and RNAi-based therapeutics.

Recent Publications

Savidge A, Zhang H, Adhav AV, Kehling AC, Sim GY, Shen Z, Fu TM, Nakanishi K. “Neurodevelopmental disorder-linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3ʹ→5ʹ trimming,” Proc. Natl. Acad. Sci. USA., 122 (46) e2524644122, 2025

Zhang H, Sim GY, Kehling AC, Annasaheb Adhav V, Savidge A, Pastore B, Tang Wen, Nakanishi K. “Target cleavage and gene silencing by Argonautes with cityRNAs,” Cell Rep., 43 114806, 2024

Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM. “DdmDE eliminates plasmid invasion by DNA-guided DNA targeting,” Cell, 187 5253-5266, 2024

Nakanishi K. “When Argonaute takes out the RNase sword,” J. Biol. Chem., 300 105499, 2024.

Sim GY, Kehling AC, Park MS, Divoky C, Zhang H, Malhotra N, Secor J, Nakanishi K. “Determining the defining lengths between mature microRNAs/small interfering RNAs and tinyRNAs,” Sci. Rep., 19761, 2023.

Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM. “Oligomerization-mediated activation of a short prokaryotic Argonaute,” Nature, 621, 154-161, 2023.

Huberdeau MQ, Shah VN, Nahar S, Neumeier J, Houle F, Bruckmann A, Gypas F, Nakanishi K, Großhans H, Meister G, Simard MJ. “A specific Argonaute phosphorylation regulates the binding to microRNAs during C. elegans development,” Cell Rep., 41, 111822, 2022.

Sim GY, Kehling AC, Park MS, Secor J, Divoky C, Zhang H, Malhotra N, Bhagdikar D, Abd El-Wahab EW, Nakanishi K. “Manganese-dependent microRNA trimming by 3’→5’ exonucleases generates 14-nucleotide or shorter tiny RNAs,” Proc. Natl. Acad. Sci. USA., 119, e2214335119, 2022.

Nakanishi K. “Anatomy of four human Argonaute proteins,” Nucleic Acids Res., 50, 6618-6638, 2022.