Exon architecture controls mRNA m 6 A suppression and gene expression.

N 6 -methyladenosine (m6 A) is the most abundant messenger RNA (mRNA) modification and plays crucial roles in diverse physiological processes. Using a massively parallel assay for m6 A (MPm6 A), we discover that m6 A specificity is globally regulated by suppressors that prevent m6 A deposition in unmethylated transcriptome regions. We identify exon junction complexes (EJCs) as m6 A suppressors that protect exon junction-proximal RNA within coding sequences from methylation and regulate mRNA stability through m6 A suppression. EJC suppression of m6 A underlies multiple global characteristics of mRNA m6 A specificity, with the local range of EJC protection sufficient to suppress m6 A 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.