Chemical inhibition of exon junction complex assembly impairs mRNA localization and neural stem cells ciliogenesis

The exon junction complex (EJC) is formed by the essential eIF4A3, MAGOH, and Y14 core proteins. It is universally deposited during splicing at exon-exon junctions. The EJC is known to impact almost every post-transcriptional regulatory step throughout the life of messenger RNAs (mRNAs) including their modifications, splicing, decay, and trafficking. Its dysregulation leads to neurodevelopmental pathologies. Here, we show that EJC-i, a compound known to block the ATPase activity of eIF4A3, inhibits de novo EJC assembly. EJC-i and targeted knockdown of either eIF4A3 or Y14 core EJC subunits lead to very similar phenotypes by impacting the destiny of mRNAs due to alterations in alternative splicing, nonsense-mediated mRNA decay, genome-wide m6A methylation, and proper localization of specific transcripts, in particular to the centrosome. Both EJC impairment methods disrupt the centrosome function, which might be responsible for mitotic arrest at prometaphase. As a small molecule that readily diffuses into cells, EJC-i is a particularly easy-to-use and versatile tool to investigate EJC functions in live cells or whole organisms that are not prone to genetic manipulation. Indeed, this property was used to disrupt ciliogenesis in primary neural stem cells.