eIF4A3 phosphorylation by CDKs affects NMD during the cell cycle. Ryu et al
Exon junction complexes (EJCs) loaded onto spliced mRNAs during splicing serve as molecular markers for various post-transcriptional gene-regulatory processes including nonsense-mediated mRNA decay (NMD). Although the composition and structure of EJCs are well characterized, the regulatory mechanism for EJC deposition remains unknown. Here, we find that threonine 163 (T163) within the RNA-binding motif of eIF4A3 (a core EJC component) is phosphorylated by cyclin-dependent protein kinases 1 and 2 in a cell cycle-dependent manner. T163 phosphorylation hinders the binding of eIF4A3 to spliced mRNAs and other EJC components. Instead, it promotes association of eIF4A3 with CWC22, which guides eIF4A3 to an active spliceosome. These molecular events ensure the fidelity of specific deposition of EJC ~20–24 nucleotides upstream of an exon-exon junction. Accordingly, NMD is affected by T163 phosphorylation. Collectively, our data provide molecular evidence that T163 phosphorylation affects EJC formation and consequently NMD efficiency in a cell cycle-dependent manner.