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

Abstract

The exon junction comple x (EJC) is f ormed b y the essential eIF4A3, MAGOH, and Y14 core proteins. It is universally deposited during splicing at e x on-e x on junctions. T he EJC is kno wn to impact almost e v er y post-transcriptional regulator y 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 no v o 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 deca y, genome-wide m6A meth ylation, 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.- The Author(s) 2025. Published by Oxford University Press.