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

Shen, Aykut, Hencel, Katarzyna, Parker, Matthew T., Scott, Robyn, Skukan, Roberta, Adesina, Aduragbemi S. ORCID: https://orcid.org/0000-0002-1029-4159, Metheringham, Carey L., Miska, Eric A., Nam, Yunsun, Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X, Simpson, Gordon G. and Akay, Alper ORCID: https://orcid.org/0000-0001-6825-4443 (2024) U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Research, 52 (15). 9139–9160. ISSN 0305-1048

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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.

Item Type:	Article
Additional Information:	Data availability statement: All raw data related to RNA sequencing is deposited at the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser/home) under the accession number PRJEB65287. All software tools and adjustments to code have been described in materials and methods. Funding information: This work was supported by a UK Research and Innovation Future Leaders Fellowship [MR/S033769/1 to A.A.]; UK Research and Innovation Biotechnology and Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership [BB/T008717/1 to A.S.]; UK Research and Innovation Biotechnology and Biological Sciences Research Council [BB/CCG1720/1, BS/E/T/000PR9818 to W.H., BB/W007673/1, BB/V010662/1 to G.G.S.]; UK Research and Innovation Medical Research Council [MR/P026028/1 to W.H.]; US National Institutes of Health [R01GM122960, R01CA258589 to Y.N.]; Welch Foundation [I-2115-20220331]; Y.N. is a Packard Fellow, Pew Scholar, and Southwestern Medical Foundation Scholar in Biomedical Research. Funding for open access charge: UKRI block grant funds under current agreements with NAR.
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging
Related URLs:	https://academic.oup.com/nar/advance-art...
Depositing User:	LivePure Connector
Date Deposited:	07 Aug 2024 16:30
Last Modified:	14 Dec 2024 01:39
URI:	https://ueaeprints.uea.ac.uk/id/eprint/96174
DOI:	10.1093/nar/gkae447

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