m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site

  1. Matthew T Parker
  2. Beth K Soanes
  3. Jelena Kusakina
  4. Antoine Larrieu
  5. Katarzyna Knop
  6. Nisha Joy
  7. Friedrich Breidenbach
  8. Anna V Sherwood
  9. Geoffrey J Barton
  10. Sebastian M Fica
  11. Brendan H Davies  Is a corresponding author
  12. Gordon Grant Simpson  Is a corresponding author
  1. University of Dundee, United Kingdom
  2. University of Leeds, United Kingdom
  3. 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.

The following data sets were generated

Article and author information

Author details

  1. Matthew T Parker

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0891-8495
  2. Beth K Soanes

    School of Biology, University of Leeds, Leeds, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Jelena Kusakina

    School of Biology, University of Leeds, Leeds, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Antoine Larrieu

    School of Biology, University of Leeds, Leeds, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Katarzyna Knop

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2636-9450
  6. Nisha Joy

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Friedrich Breidenbach

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9610-1927
  8. Anna V Sherwood

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Geoffrey J Barton

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9014-5355
  10. Sebastian M Fica

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Brendan H Davies

    School of Biology, University of Leeds, Leeds, United Kingdom
    For correspondence
    b.h.davies@leeds.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  12. Gordon Grant Simpson

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    For correspondence
    g.g.simpson@dundee.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6744-5889

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.

Reviewing Editor

  1. Jonathan P Staley, University of Chicago, United States

Publication history

  1. Received: March 21, 2022
  2. Accepted: November 20, 2022
  3. Accepted Manuscript published: November 21, 2022 (version 1)

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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  1. Matthew T Parker
  2. Beth K Soanes
  3. Jelena Kusakina
  4. Antoine Larrieu
  5. Katarzyna Knop
  6. Nisha Joy
  7. Friedrich Breidenbach
  8. Anna V Sherwood
  9. Geoffrey J Barton
  10. Sebastian M Fica
  11. Brendan H Davies
  12. Gordon Grant Simpson
(2022)
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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