Decoding noncanonical intron splicing rules in Euglena

September 23, 2025

A new sequence logic for eukaryotic gene expression

A collaborative research group, including scientists from the RIKEN CSRS, the University of Tokyo, Euglena Co., Ltd., Yamagata University, Tsuruoka College of Technology, Kochi University, Nagasaki University, and Yokohama City University has uncovered that Euglena employs a unique splicing strategy in mRNA processing. Unlike conventional eukaryotes that predominantly follow the GT–AG rule for intron splicing, Euglena utilizes a large number of introns that obey an entirely different sequence logic. This study reveals that Euglena co-dominantly uses both conventional and nonconventional introns, marking the first molecular genetic evidence of such dual splicing systems in a eukaryotic organism. By combining genome editing techniques with structural modeling and enzymatic assays, the team identified a specific DNA sequence signature required for noncanonical splicing. This discovery opens new possibilities for synthetic biology applications, such as the programmable control of gene expression through the insertion of synthetic introns.

Also, the species studied, Euglena gracilis, is a microalga increasingly used in health food and biofuel production. A precise understanding of its gene structure is essential for genetic improvement using genome editing. This research is expected to facilitate the identification and modification of metabolic pathways involved in the production of valuable compounds in Euglena, and contribute to the development of traits that enhance biomass productivity for carbon fixation and resource utilization.

 

Original article

Proceedings of the National Academy of Sciences　doi: 10.1073/pnas.2509937122

T. Nomura, J.-S. Kim, O. Iwata, K. Yamada, K. Atsuji, Y. Uehara-Yamaguchi, T. Yoshida, K. Inoue, K. Takahagi, T. Sakurai, K. Shinozaki, T. Ito, K. Suzuki, K. Goda, K. Mochida,

"Genetic dissection of nonconventional introns reveals co-dominant noncanonical splicing code in Euglena".

Contact

Toshihisa Nomura; Senior Visiting Scientist
June-Sik Kim; Research Scientist
Keiichi Mochida; Team Director
Bioproductivity Informatics Research Team