Genetic dissection of nonconventional introns reveals codominant noncanonical splicing code in <i>Euglena</i>
Pre-mRNA splicing is essential for eukaryotic gene expression and is achieved through the accurate recognition of exon-intron boundaries. Although nonconventional introns, which do not follow the conventional GT-AG splicing rule, have been identified in several species, these introns are typically rare in any given genome. Here, we demonstrate the widespread occurrence of nonconventional introns (71.8% of all introns) in the <i>Euglena agilis</i> genome and identify consensus motifs at these nonconventional exon-intron boundaries. We assessed the splicing efficiency of nonconventional introns and variants with point mutations via genomic knock-in within the second exon of <i>Glucan synthase-like 2</i> in <i>Euglena gracilis</i> and genetically defined the sequence signature (5'-N<sub>3</sub>CDG-/-CH'GN<sub>5-6</sub>|R<sub>exon</sub>-3') required for their proper splicing. This signature is present in 61.2% of all nonconventional introns detected in the <i>E. agilis</i> genome. Accordingly, we present a noncanonical splicing code for <i>Euglena</i> introns, highlighting the global coexistence of dual splicing rules for conventional and nonconventional introns.
Authors
- June‐Sik Kim (ORCID: https://orcid.org/0000-0002-4703-609X)
- Keisuke Goda (ORCID: https://orcid.org/0000-0001-6302-6038)
- Komaki Inoue (ORCID: https://orcid.org/0000-0002-7645-7862)
- Kotaro Takahagi (ORCID: https://orcid.org/0000-0002-1210-710X)
- Keiichi Mochida (ORCID: https://orcid.org/0000-0003-1299-0024)
- Yukiko Uehara‐Yamaguchi
- Toshihisa Nomura (ORCID: https://orcid.org/0000-0002-6806-3708)
- Toshinori Yoshida (ORCID: https://orcid.org/0000-0003-2476-7794)
- Kohei Atsuji
- Osamu Iwata (ORCID: https://orcid.org/0000-0002-5180-4573)
- Takuro Ito (ORCID: https://orcid.org/0000-0001-5043-1886)
- Tetsuya Sakurai (ORCID: https://orcid.org/0000-0002-5789-7547)
- Koji Yamada (ORCID: https://orcid.org/0000-0002-2049-0882)
- Kengo Suzuki
- Kazuo Shinozaki (ORCID: https://orcid.org/0000-0002-6317-9867)
Institutions
- Yamagata University (JP)
- Kihara Institute for Biological Research (JP)
- University of California, Los Angeles (US)
- Okayama University (JP)
- Wuhan University of Technology (CN)
- Tohoku University (JP)
- Wuhan University (CN)
- Manx National Heritage (IM)
- RIKEN Center for Sustainable Resource Science (JP)
- Innovation Cluster (Canada) (CA)
- Nagasaki University (JP)
- National Institute of Technology, Tsuruoka College (JP)
- The University of Tokyo (JP)
- Kōchi University (JP)
- Yokohama City University (JP)
Publication Details
- Journal
- Proceedings of the National Academy of Sciences
- Published
- 2025-09-23
- DOI
- https://doi.org/10.1073/pnas.2509937122
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 0.00