Exon-intron boundary inhibits m 6 A deposition, enabling m 6 A distribution hallmark, longer mRNA half-life and flexible protein coding.

Regional bias of N 6 -methyladenosine (m 6 A) mRNA modification avoiding splice site region, calls for an open hypothesis whether exon-intron boundary could affect m 6 A deposition. By deep learning modeling, we find that exon-intron boundary represses a proportion (12% to 34%) of m 6 A deposition at adjacent exons (~100 nt to splice site). Experiments validate that m 6 A signal increases once the host gene does not undergo pre-mRNA splicing to produce the same mRNA. Inhibited m 6 A sites have higher m 6 A enhancers and lower m 6 A silencers locally and show high heterogeneity at different exons genome-widely, with only a small proportion (12% to 15%) of exons showing strong inhibition, enabling more stable mRNAs and flexible protein coding. m 6 A is majorly responsible for why mRNAs with more exons be more stable. Exon junction complex (EJC) only partially contributes to this exon-intron boundary m 6 A inhibition in some short internal exons, highlighting additional factors yet to be identified.