U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs

• Published in: Nucleic acids research Vol. 52; no. 15; pp. 9139 - 9160
• Main Authors: Shen, Aykut, Hencel, Katarzyna, Parker, Matthew T, Scott, Robyn, Skukan, Roberta, Adesina, Aduragbemi S, Metheringham, Carey L, Miska, Eric A, Nam, Yunsun, Haerty, Wilfried, Simpson, Gordon G, Akay, Alper
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 27.08.2024
• Subjects: Adenosine - analogs & derivatives; Adenosine - genetics; Adenosine - metabolism; Alternative Splicing; Animals; Caenorhabditis elegans - genetics; Caenorhabditis elegans - metabolism; Caenorhabditis elegans Proteins - genetics; Caenorhabditis elegans Proteins - metabolism; Humans; Methyltransferases - genetics; Methyltransferases - metabolism; RNA and RNA-protein complexes; RNA Precursors - genetics; RNA Precursors - metabolism; RNA Splice Sites; RNA Splicing; RNA, Small Nuclear - genetics; RNA, Small Nuclear - metabolism; Spliceosomes - genetics; Spliceosomes - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae447

Abstract pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5′ splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3′ cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5′ splice sites with +4A. Finally, we show that editing endogenous 5′ splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5′ splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing. Graphical Abstract Graphical Abstract