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FTO controls reversible m6Am RNA methylation during snRNA biogenesis

Nature Chemical Biology volume 15, pages 340–347 (2019)Cite this article

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Abstract

Small nuclear RNAs (snRNAs) are core spliceosome components and mediate pre-mRNA splicing. Here we show that snRNAs contain a regulated and reversible nucleotide modification causing them to exist as two different methyl isoforms, m1 and m2, reflecting the methylation state of the adenosine adjacent to the snRNA cap. We find that snRNA biogenesis involves the formation of an initial m1 isoform with a single-methylated adenosine (2′-O-methyladenosine, Am), which is then converted to a dimethylated m2 isoform (N6,2′-O-dimethyladenosine, m6Am). The relative m1 and m2 isoform levels are determined by the RNA demethylase FTO, which selectively demethylates the m2 isoform. We show FTO is inhibited by the oncometabolite d-2-hydroxyglutarate, resulting in increased m2-snRNA levels. Furthermore, cells that exhibit high m2-snRNA levels show altered patterns of alternative splicing. Together, these data reveal that FTO controls a previously unknown central step of snRNA processing involving reversible methylation, and suggest that epitranscriptomic information in snRNA may influence mRNA splicing.

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Fig. 1: FTO selectively demethylates small nuclear RNAs.
Fig. 2: Reversible N6,2′-O-dimethyladenosine (m6Am) in small nuclear RNAs.
Fig. 3: m2-snRNAs are reversibly regulated in oncometabolite-dependent cancer models.
Fig. 4: m2-snRNAs are incorporated into snRNPs.

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Code availability

All custom code used in this study can be obtained upon request from the corresponding author.

Data availability

Sequencing data that support the findings of this study have been deposited in the NCBI GEO database under accession number GSE107872. Other data shown in the article are available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank K. Keshari (MSKCC) for UOK262 cells. This work was supported by NIH grants R01DA037755 and R01CA186702 (S.R.J.), R01GM123977 (H.G.), R01NS102451 (L.P.), P01HD67244, P01HD067244 (M.S.), and UO1HL121828 (S.S.G.), by the French Centre National de la Recherche Scientifique (T.G., J.-J.V., F.D.), DFG Priority Program grant RE2796/3-2 (A.R.) and by a DFG Research Fellowship (J.M.).

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  1. Jan Mauer

    Present address: BioMed X Innovation Center, Heidelberg, Germany

  2. These authors contributed equally: Miriam Sindelar, Vladimir Despic.

Authors and Affiliations

  1. Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA

    Jan Mauer, Miriam Sindelar, Vladimir Despic, Ben R. Hawley, Steven S. Gross & Samie R. Jaffrey

  2. IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France

    Théo Guez, Jean-Jacques Vasseur & Françoise Debart

  3. Department of Chemistry, Institute of Biochemistry, University of Muenster, Muenster, Germany

    Andrea Rentmeister

  4. Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA

    Livio Pellizzoni

  5. Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA

    Hani Goodarzi

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Contributions

S.R.J., L.P. and J.M. designed the experiments. J.M. carried out the experiments. F.D., J.-J.V. and T.G. synthesized modified oligonucleotides. A.R. produced hTGS1. S.S.G. and M.S. carried out mass spectrometry analysis. V.D. performed analysis of snRNA and snRNP stability, binding and assembly. B.R.H. helped with RNA extraction and sample preparation for mass spectrometry analysis. H.G. carried out the computational splicing analysis. S.R.J. and J.M. wrote the manuscript with input from all co-authors.

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Correspondence to Samie R. Jaffrey.

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S.R.J. is scientific founder of, advisor to, and owns equity in Gotham Therapeutics.

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Supplementary Figures 1–12

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Supplementary Table 1

List of 26,087 annotated transcription start sites.

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Mauer, J., Sindelar, M., Despic, V. et al. FTO controls reversible m6Am RNA methylation during snRNA biogenesis. Nat Chem Biol 15, 340–347 (2019). https://doi.org/10.1038/s41589-019-0231-8

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