Abstract N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNA. Increasing evidence shows that m6A is involved in the biological functions of cancer cells, including proliferation, invasion, metastasis, and drug resistance. Dysregulation of m6A deposition and its associated machinery, including writers, erasers and readers, is observed in multiple cancer types, and the dysregulation profiles have potential as diagnostic, prognostic and/or predictive biomarkers. In healthy cells, m6A modifications are installed co-transcriptionally by the writer enzyme METTL3, resulting in an enrichment of m6A in the 3’UTR of genes. For many years, the mechanistic origin for the m6A enrichment in the 3’UTR was unclear. Recently, the Gregory lab and others have developed a model where the exon junction complex (EJC) plays a key role in directing m6A deposition by hindering access of METTL3 to short exons and exon/intron junctions. In this study, we build on this model using a novel, proximity-barcoding based assay (EpiPlex™) for the simultaneous detection of m6A and inosine. Working with HEK293T cells, we modulated the activity of a central component of the EJC, the RNA helicase EIF4A3. Both genetic knockdown and chemical inhibition of EIF4A3 resulted in increased m6A levels and more diffuse localization at the 3’UTR. New m6A sites appear on short exons and near exon/intron junctions. These data corroborate the necessity of EIF4A3 for EJC assembly and confirm the model that the EJC prevents METTL3 from accessing and methylating exon junctions. Additionally, we find that blocking of the exon junction is reliant on EIF4A3’s helicase activity. Although the role of EJC in the cell cycle and cancer are still investigational, it is likely that m6A dysregulation is induced by aberrant EJC function, which presents a potential molecular mechanism for the dysregulation of multiple genetic pathways in cancer progression. Citation Format: Andrew Price, Erdem Sendinc, Byron Purse, Richard I Gregory, Gudrun Stengel. Binding of the exon junction complex shapes the landscape of m6A in RNA - a possible source of m6A dysregulation in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A011.
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