Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation
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 regul...
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| Format: | Article |
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eLife Sciences Publications Ltd
2022-01-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/72867 |
| _version_ | 1818019168140656640 |
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| author | Maxim I Maron Alyssa D Casill Varun Gupta Jacob S Roth Simone Sidoli Charles C Query Matthew J Gamble David Shechter |
| author_facet | Maxim I Maron Alyssa D Casill Varun Gupta Jacob S Roth Simone Sidoli Charles C Query Matthew J Gamble David Shechter |
| author_sort | Maxim I Maron |
| collection | DOAJ |
| description | 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. Taken together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns. |
| first_indexed | 2024-04-14T07:47:46Z |
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| id | doaj.art-45b87284ee8349d28110b43dc16d75b2 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:47:46Z |
| publishDate | 2022-01-01 |
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| series | eLife |
| spelling | doaj.art-45b87284ee8349d28110b43dc16d75b22022-12-22T02:05:16ZengeLife Sciences Publications LtdeLife2050-084X2022-01-011110.7554/eLife.72867Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylationMaxim I Maron0https://orcid.org/0000-0001-7809-5888Alyssa D Casill1Varun Gupta2https://orcid.org/0000-0001-5330-0486Jacob S Roth3https://orcid.org/0000-0003-0521-8677Simone Sidoli4https://orcid.org/0000-0001-9073-6641Charles C Query5https://orcid.org/0000-0002-7692-2496Matthew J Gamble6https://orcid.org/0000-0002-8107-0523David Shechter7https://orcid.org/0000-0001-9388-6004Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Cell Biology, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Cell Biology, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, United States; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, United StatesProtein 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. Taken together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns.https://elifesciences.org/articles/72867PRMT5PRMT1retained detained intronsRNA processingsnRNPA549 |
| spellingShingle | Maxim I Maron Alyssa D Casill Varun Gupta Jacob S Roth Simone Sidoli Charles C Query Matthew J Gamble David Shechter Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation eLife PRMT5 PRMT1 retained detained introns RNA processing snRNP A549 |
| title | Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation |
| title_full | Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation |
| title_fullStr | Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation |
| title_full_unstemmed | Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation |
| title_short | Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation |
| title_sort | type i and ii prmts inversely regulate post transcriptional intron detention through sm and chtop methylation |
| topic | PRMT5 PRMT1 retained detained introns RNA processing snRNP A549 |
| url | https://elifesciences.org/articles/72867 |
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