Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing

Mateusz Mendel; Kamila Delaney; Radha Raman Pandey; Kuan-Ming Chen; Joanna M Wenda; Cathrine Broberg Vågbø; Florian A Steiner; David Homolka; Ramesh S Pillai

doi:10.1016/j.cell.2021.03.062

Splice site m⁶A methylation prevents binding of U2AF35 to inhibit RNA splicing

Cell. 2021 Jun 10;184(12):3125-3142.e25. doi: 10.1016/j.cell.2021.03.062. Epub 2021 Apr 29.

Authors

Mateusz Mendel¹, Kamila Delaney¹, Radha Raman Pandey¹, Kuan-Ming Chen¹, Joanna M Wenda¹, Cathrine Broberg Vågbø², Florian A Steiner¹, David Homolka³, Ramesh S Pillai⁴

Affiliations

¹ Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
² Proteomics and Modomics Experimental Core (PROMEC), Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) and St. Olavs Hospital Central Staff, Trondheim, Norway.
³ Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Electronic address: david.homolka@unige.ch.
⁴ Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Electronic address: ramesh.pillai@unige.ch.

Abstract

The N⁶-methyladenosine (m⁶A) RNA modification is used widely to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (the ortholog of mouse METTL16) deposits an m⁶A mark on the 3' splice site (AG) of the S-adenosylmethionine (SAM) synthetase pre-mRNA, which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet and acts as an m⁶A-mediated switch to stop SAM production and regulate its homeostasis. Although the mammalian SAM synthetase pre-mRNA is not regulated via this mechanism, we show that splicing inhibition by 3' splice site m⁶A is conserved in mammals. The modification functions by physically preventing the essential splicing factor U2AF35 from recognizing the 3' splice site. We propose that use of splice-site m⁶A is an ancient mechanism for splicing regulation.

Keywords: 3' splice site; METT-10; METTL16; SAM homeostasis; SAM synthetase; U2AF35/65; U6 snRNA; m(6)A; spermatogenesis; splicing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adenosine / analogs & derivatives*
Adenosine / metabolism
Amino Acid Sequence
Animals
Base Sequence
Caenorhabditis elegans / genetics
Conserved Sequence / genetics
Diet
HeLa Cells
Humans
Introns / genetics
Methionine Adenosyltransferase
Methylation
Methyltransferases / chemistry
Mice
Mutation / genetics
Nucleic Acid Conformation
Protein Binding
RNA Precursors / chemistry
RNA Precursors / genetics
RNA Precursors / metabolism
RNA Splice Sites / genetics*
RNA Splicing / genetics*
RNA, Messenger / genetics
RNA, Messenger / metabolism
RNA, Small Nuclear
S-Adenosylmethionine
Splicing Factor U2AF / metabolism*
Transcriptome / genetics

Substances

RNA Precursors
RNA Splice Sites
RNA, Messenger
RNA, Small Nuclear
Splicing Factor U2AF
U2AF1 protein, human
U6 small nuclear RNA
S-Adenosylmethionine
N-methyladenosine
METTL16 protein, human
Methyltransferases
Methionine Adenosyltransferase
Adenosine

Grants and funding

P40 OD010440/OD/NIH HHS/United States