Exon junction complex shapes the m6A epitranscriptome.

N6-methyladenosine (m⁶A), the most abundant modification of mRNA, is essential for normal development and dysregulation promotes cancer. m⁶A is highly enriched in the 3' untranslated region (UTR) of a large subset of mRNAs to influence mRNA stability and/or translation. However, the mechanism responsible for the observed m⁶A distribution remains enigmatic. Here we find the exon junction complex shapes the m⁶A landscape by blocking METTL3-mediated m⁶A modification close to exon junctions within coding sequence (CDS). Depletion of EIF4A3, a core component of the EJC, causes increased METTL3 binding and m⁶A modification of short internal exons, and sites close to exon-exon junctions within mRNA. Reporter gene experiments further support the role of splicing and EIF4A3 deposition in controlling m⁶A modification via the local steric blockade of METTL3. Our results explain how characteristic patterns of m⁶A mRNA modification are established and uncover a role of the EJC in shaping the m⁶A epitranscriptome. Here the authors show the exon junction complex (EJC) component, EIF4A3, locally restricts METTL3- mediated mRNA methylation at exon junctions to explain the observed widespread enrichment of m6A modification in 3' untranslated regions. [ABSTRACT FROM AUTHOR]