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.

PRMT5 regulates ATF4 transcript splicing and oxidative stress response

“…3 e). Collectively, although we cannot exclude possible posttranscriptional conversion of V1 to V2 upon DRB treatment, it is likely that the rapid drop in V1 levels upon DRB treatment is transcript stability-related, as DRB also inhibits kinase activity essential for the splicing process [ 35 ] and PRMT1 and PRMT5 have been reported to regulate intron retention post-transcriptionally [ 36 ].…”

“…PRMT5 depletion or inhibition leads to aberrant splicing and transcriptome changes [ 7 , 8 , 10 , 32 , 33 ]. Interestingly, a recent study on PRMT5 regulated splicing mechanisms indicates a critical role for the spliceosome component SmB protein methylation by PRMT5 [ 36 ]. We found that PRMT5 inhibition or knockdown resulted in downregulation of ATF4 and downstream ATF4 regulated UPR genes.…”

Regulation of Pre-mRNA Splicing: Indispensable Role of Post-Translational Modifications of Splicing Factors

“…Methylation is a post-translational modification that functions primarily in cell signaling and cell fate decisions [ 180 , 181 , 182 , 183 ]. However, recent studies showed that methylation might also be involved in regulation of pre-mRNA splicing [ 184 , 185 , 186 , 187 , 188 , 189 ]. Methylation is executed by members of the PRMT family and the putative arginine methyltransferase NDUFAF7.…”

DNA Repair and Therapeutic Strategies in Cancer Stem Cells

“…Indeed, the core spliceosome components, SmB and SmD1/3, are key PRMT5 substrates enabling the assembly of the mature core small nuclear ribonucleoproteins (snRNPs) [ 228 ]. The importance of PRMT5 for splicing has since been demonstrated by numerous approaches including genetic knockout and enzymatic inhibition [ 223 , 224 , 225 , 229 , 230 ]. More importantly, there is a growing appreciation that PRMT5 regulates splicing events that contribute to genome stability in stem cells.…”