PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression

The Exon Junction Complex (EJC) decorates RNA exon-exon junctions and modulates mRNA fate at multiple post-transcriptional steps until its disassembly during translation. Our investigation of the EJC disassembly factor PYM1 in human embryonic kidney 293 (HEK293) cells show that the EJC-PYM1 interaction is required for translation-independent EJC destabilization but not for translation-dependent disassembly. Surprisingly, PYM1 interaction deficient EJCs are enriched on locations away from canonical EJC binding site, particularly on transcripts with no or few introns. Such non-canonical EJCs are capable of inducing nonsense-mediated mRNA decay when present downstream of stop codons. Suppression of PYM1 in human cells, including by previously reported PYM1-flavivirus capsid protein interaction, stabilizes mRNAs with fewer and longer exons that localize to endoplasmic reticulum associated TIS-granules. In summary, PYM1 limits non-canonical EJC and thereby acts as an EJC specificity factor that is hijacked by flaviviruses to reshape host cell mRNA regulation.