m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site
- University of Dundee, United Kingdom
- University of Leeds, United Kingdom
- University of Oxford, United Kingdom
Abstract
Alternative splicing of messenger RNAs is associated with the evolution of developmentally complex eukaryotes. Splicing is mediated by the spliceosome, and docking of the pre-mRNA 5' splice site into the spliceosome active site depends upon pairing with the conserved ACAGA sequence of U6 snRNA. In some species, including humans, the central adenosine of the ACAGA box is modified by N6 methylation, but the role of this m6A modification is poorly understood. Here we show that m6A modified U6 snRNA determines the accuracy and efficiency of splicing. We reveal that the conserved methyltransferase, FIO1, is required for Arabidopsis U6 snRNA m6A modification. Arabidopsis fio1 mutants show disrupted patterns of splicing that can be explained by the sequence composition of 5' splice sites and cooperative roles for U5 and U6 snRNA in splice site selection. U6 snRNA m6A influences 3' splice site usage. We generalise these findings to reveal two major classes of 5' splice site in diverse eukaryotes, which display anti-correlated interaction potential with U5 snRNA loop 1 and the U6 snRNA ACAGA box. We conclude that U6 snRNA m6A modification contributes to the selection of degenerate 5' splice sites crucial to alternative splicing.
Data availability
Illumina sequencing data from the genetic screen that identified fio1-4 is available from ENA accession PRJEB51468. Col-0, fip37-4 and fio1-1 nanopore DRS data is available from ENA accession PRJEB51364. Col-0 and fio1-3 Illumina RNA-Seq data is available from ENA accession PRJEB51363.
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Mutant screen of early flowering Arabidopsis EMS mutants with increased MAF2 intron retentionEuropean Nucleotide Archive (EMBL-EBI), PRJEB51468.
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Nanopore direct RNA sequencing of Col-0 and fio1-3 mutant ArabidopsisEuropean Nucleotide Archive (EMBL-EBI), PRJEB51364.
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Illumina RNA sequencing of Col-0 and fio1-3 mutant ArabidopsisEuropean Nucleotide Archive (EMBL-EBI), PRJEB51363.
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Identification and Function Research of Methyltransferase of N6 Methyladenine in PlantsGenome Sequence Archive (CNCB), CRA004052.
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N6-Adenosine (m6A) Methylation profiling in Arabidopsis thaliana wild-type and fio1-2 by nanopore DRS sequencingEuropean Nucleotide Archive (EMBL-EBI), PRJNA749003.
Article and author information
Author details
Friedrich Breidenbach
Gordon Grant Simpson
Funding
Biotechnology and Biological Sciences Research Council (BB/W002302/1)
- Geoffrey J Barton
- Gordon Grant Simpson
Wellcome Trust (220212/Z/20/Z)
- Sebastian M Fica
Global Challenges Research Fund (University of Dundee Global Challenges Research Fund)
- Geoffrey J Barton
- Gordon Grant Simpson
Biotechnology and Biological Sciences Research Council (BB/M010066/1)
- Geoffrey J Barton
- Gordon Grant Simpson
Biotechnology and Biological Sciences Research Council (BB/M004155/1)
- Geoffrey J Barton
- Gordon Grant Simpson
Biotechnology and Biological Sciences Research Council (BB/W007673/1)
- Geoffrey J Barton
- Gordon Grant Simpson
Biotechnology and Biological Sciences Research Council (BB/M000338/1)
- Brendan H Davies
Biotechnology and Biological Sciences Research Council (BB/W007967/1)
- Brendan H Davies
Biotechnology and Biological Sciences Research Council (BB/T007222/1)
- Beth K Soanes
- Brendan H Davies
HORIZON EUROPE Marie Sklodowska-Curie Actions (799300)
- Katarzyna Knop
HORIZON EUROPE Marie Sklodowska-Curie Actions (896598)
- Nisha Joy
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Parker et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site
eLife 11:e78808.
https://doi.org/10.7554/eLife.78808
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