Exon architecture controls mRNA m⁶A suppression and gene expression

N⁶-methyladenosine (m⁶A) is the most abundant messenger RNA (mRNA) modification and plays crucial roles in diverse physiological processes. Using a massively parallel assay for m⁶A (MPm⁶A), we discover that m⁶A specificity is globally regulated by suppressors that prevent m⁶A deposition in unmethylated transcriptome regions. We identify exon junction complexes (EJCs) as m⁶A suppressors that protect exon junction-proximal RNA within coding sequences from methylation and regulate mRNA stability through m⁶A suppression. EJC suppression of m⁶A underlies multiple global characteristics of mRNA m⁶A specificity, with the local range of EJC protection sufficient to suppress m⁶A deposition in average-length internal exons but not in long internal and terminal exons. EJC-suppressed methylation sites colocalize with EJC-suppressed splice sites, which suggests that exon architecture broadly determines local mRNA accessibility to regulatory complexes.