Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation
- Albert Einstein College of Medicine, United States
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.
Article and author information
Author details
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
- Kristen W Lynch, University of Pennsylvania, United States
Version history
- Received: August 6, 2021
- Preprint posted: August 20, 2021 (view preprint)
- Accepted: January 3, 2022
- Accepted Manuscript published: January 5, 2022 (version 1)
- 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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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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