Research Description

Small noncoding RNAs, including microRNAs (miRNAs), regulate gene expression by guiding Argonaute (AGO) proteins to complementary target RNAs through the RNA interference (RNAi) pathway. 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 direct RNA cleavage. Dysregulation of this pathway contributes to numerous human diseases, including neurodevelopmental disorders and cancer.

Research in the Nakanishi laboratory aims to elucidate the molecular mechanisms that govern RISC assembly, activation, and function. Our recent cryo-electron microscopy studies revealed the structural basis of human AGO2 RISC assembly and maturation (Zhang et al., Molecular Cell, 2026).

Another major focus of the laboratory is understanding the functional specialization of human AGO paralogs. We discovered that AGO3, previously considered catalytically inactive, becomes a highly efficient slicer when loaded with specific short guide RNAs, termed cleavage-inducing tiny RNAs (cityRNAs). This discovery established a new paradigm for RNA-guided gene regulation and provides a foundation for developing programmable RNA-targeting technologies with improved specificity.

To address these questions, the laboratory integrates cryo-electron microscopy, biochemistry, biophysics, molecular and cell biology, and quantitative imaging. By combining structural biology with mechanistic and cellular studies, we seek to uncover fundamental principles of RNA-mediated gene regulation and translate these discoveries into next-generation RNAi-based therapeutics.