PYM1 controls non-canonical EJC occupancy and maintains homeostatic expression of membrance targeted transcripts
During pre-mRNA splicing in the nucleus, the spliceosome deposits the Exon Junction Complex (EJC) ~24 nucleotides upstream of exon-exon junctions. The EJC core thus deposited comprises of EIF4A3, RBM8A and MAGOH and remains stably bound to RNA to modulate mRNA fate at multiple post-transcriptional steps until its disassembly during translation. Such EJC disassembly is proposed to be mediated by PYM1, a factor that can bind both the ribosome and the RBM8A/MAGOH heterodimer of the EJC core. Here, we investigated the role of PYM1 in regulating EJC binding in human embryonic kidney 293 (HEK293) cells using a MAGOH mutant that assembles into EJC but is impaired in PYM1 interaction. We find that EJCs lacking PYM1 interaction show no defect in translation dependent disassembly. Surprisingly, PYM1 interaction deficient EJCs are enriched on sites away from the canonical EJC binding position including on transcripts without introns or fewer and longer exons. Additionally, acute reduction and elevation of PYM1 levels in HEK293 cells result in a modest NMD inhibition and stabilization of mRNAs that localize to endoplasmic reticulum associated TIS-granules and are characterized by fewer and longer exons. These gene expression changes are mirrored in flavivirus infected cells, suggesting a potential role for PYM1 in host-pathogen interactions, as flaviviruses are known to target this protein. Overall design: RIPiT-Seq of EJC bound RNA from HEK293 cells expressing FLAG-tagged MAGOH and RNA-seq from cells depleted of PYM1, cells overexpressing PYM1, cells overexpressing PYM1 deltaN and control cells.