Genetic dissection of nonconventional introns reveals codominant noncanonical splicing code in Euglena

• 成果类型: Article
• 署名作者: Nomura, Toshihisa; Kim, June - Sik; Iwata, Osamu; Yamada, Koji; Atsuji, Kohei; Uehara-Yamaguchi, Yukiko; Yoshida, Takuhiro; Inoue, Komaki; Takahagi, Kotaro; Sakurai, Tetsuya; Shinozaki, Kazuo; Ito, Takuro; Suzuki, Kengo; Goda, Keisuke; Mochida, Keiichi
• 署名单位: RIKEN; RIKEN; Yamagata University; Okayama University; Yokohama City University; Kochi University; University of Tokyo; Wuhan University; University of California System; University of California Los Angeles; Tohoku University; Nagasaki University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9849
• DOI: 10.1073/pnas.2509937122
• 发表日期: 2025-09-30
• 关键词: messenger-rna; minor class; spliceosome; generation; sequence; insights; tubulin; genomes; alpha; u12

摘要

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 Euglena agilis 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 Glucan synthase-like 2 in Euglena gracilis and genetically defined the sequence signature (5 '- N3CDG-/- CH ' GN5-6|Rexon-3 ') required for their proper splicing. This signature is present in 61.2% of all nonconventional introns detected in the E. agilis genome. Accordingly, we present a noncanonical splicing code for Euglena introns, highlighting the global coexistence of dual splicing rules for conventional and nonconventional introns.