Productive mRNA chromatin escape is promoted by PRMT5 activity - mRNA Seq PRMT5 pICln RIOK1 CoPR5 kd
Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) —but not type I PRMT inhibition—leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export. Overall design: To measure transcriptomic consequences of PRMT5 cofactor knockdowns, CRISPRi knockdown with dCas9-KRAB-MeCP2 was performed. Two guide RNAs (gRNA) per target were made and mRNA-seq was performed with poly-A capture non-directional library preparation and PE150 reads (9GB total data, roughly 30M PE reads per sample) Raw data was mapped to hg38 using STAR in the nf-core/rnaseq pipeline and length-normalized counts called by salmon. DESeq2 was then used for differential abundance of the knockdown vs sgScr (scrambled guideRNA) control