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., Metheringham, Carey L., Miska, Eric A., Nam, Yunsun, Haerty, Wilfried, Simpson, Gordon G. and Akay, Alper (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

Preview

PDF (Shen_etal_2024_NAR_gkae447) - Published Version Available under License Creative Commons Attribution. Download (4MB) | Preview

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:	06 Feb 2025 12:09
URI:	https://ueaeprints.uea.ac.uk/id/eprint/96174
DOI:	10.1093/nar/gkae447

Downloads

Actions (login required)

View Item