High throughput sequencing identifies alternative splicing events regulated by PRMT9

The human genome encodes a family of nine protein arginine methyltransferases (PRMT1-9). Different members of this enzyme family catalyze different types of protein methylation at the terminal nitrogen atoms of arginine residues, forming monomethylated arginine (MMA), asymmetrically dimethylated arginine (ADMA) and symmetrically dimethylated arginine (SDMA). The last member of this family, PRMT9, is characterized in detail here. We identify two spliceosome-associated proteins, SAP145 (SF3B2) and SAP49 (SF3B4), as PRMT9 binding partners, linking PRMT9 to U2snRNP maturation. We show that SAP145 is methylated by PRMT9 at arginine 508 (R508). Amino acid analysis and a methyl-specific antibody revealed the formation of MMA and SDMA, and PRMT9 thus joins PRMT5 as the only mammalian enzymes that can deposit the SDMA mark. Methylation of the SAP145R508 generates a binding site for the Tudor domain of SMN, and RNA-seq analysis reveals gross splicing changes when PRMT9 levels are attenuated. These studies identify PRMT9 as a non-histone methyltransferase that primes the U2snRNP for interaction with SMN. RNA sequencing was carried out using RNA samples from two biological replicates of control and PRMT9 knockdown HeLa cells.