Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation

Abstract

Protein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I PRMT enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed Splicing Kinetics and Transcript Elongation Rates by Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhibition resulted in altered splicing rates. Surprisingly, co-transcriptional splicing kinetics did not correlate with final changes in splicing of polyadenylated RNA. This was particularly true for retained introns (RI). By using actinomycin D to inhibit ongoing transcription, we determined that PRMTs post-transcriptionally regulate RI. Subsequent proteomic analysis of both PRMT-inhibited chromatin and chromatin-associated polyadenylated RNA identified altered binding of many proteins, including the Type I substrate, CHTOP, and the Type II substrate, SmB. Targeted mutagenesis of all methylarginine sites in SmD3, SmB, and SmD1 recapitulated splicing changes seen with Type II PRMT inhibition, without disrupting snRNP assembly. Similarly, mutagenesis of all methylarginine sites in CHTOP recapitulated the splicing changes seen with Type I PRMT inhibition. Examination of subcellular fractions further revealed that RI were enriched in the nucleoplasm and chromatin. Together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns.

Data availability

Raw data for RNA seq and SKaTER seq is deposited under GEO (GSE163421)Raw data for chromatin-associated poly(A) LC-MS/MS is deposited under Chorus (1729).All code used to generate data in this manuscript can be found here: https://github.com/Shechterlab/PRMTsRegulatePostTranscriptionalDI.

The following data sets were generated

Article and author information

Author details

  1. Maxim I Maron

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7809-5888
  2. Alyssa D Casill

    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Varun Gupta

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jacob S Roth

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Simone Sidoli

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Charles C Query

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7692-2496
  7. Matthew J Gamble

    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. David Shechter

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
    For correspondence
    david.shechter@einsteinmed.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9388-6004

Funding

National Institute of General Medical Sciences (R01GM108646)

  • David Shechter

National Institute of General Medical Sciences (R01GM57829)

  • Charles C Query

National Institute of General Medical Sciences (R01GM134379)

  • Matthew J Gamble

American Lung Association (LCD-564723)

  • David Shechter

Irma T. Hirschl Trust

  • Matthew J Gamble
  • David Shechter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kristen W Lynch, University of Pennsylvania, United States

Publication history

  1. Received: August 6, 2021
  2. Preprint posted: August 20, 2021 (view preprint)
  3. Accepted: January 3, 2022
  4. Accepted Manuscript published: January 5, 2022 (version 1)
  5. Version of Record published: January 18, 2022 (version 2)

Copyright

© 2022, Maron 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. Maxim I Maron
  2. Alyssa D Casill
  3. Varun Gupta
  4. Jacob S Roth
  5. Simone Sidoli
  6. Charles C Query
  7. Matthew J Gamble
  8. David Shechter
(2022)
Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation
eLife 11:e72867.
https://doi.org/10.7554/eLife.72867

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