Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - 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. 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