Exon-intron boundary inhibits m6A deposition, enabling m6A distribution hallmark, longer mRNA half-life and flexible protein coding

Abstract

Regional bias of N⁶-methyladenosine (m⁶A) mRNA modification avoiding splice site region, calls for an open hypothesis whether exon-intron boundary could affect m⁶A deposition. By deep learning modeling, we find that exon-intron boundary represses a proportion (12% to 34%) of m⁶A deposition at adjacent exons (~100 nt to splice site). Experiments validate that m⁶A signal increases once the host gene does not undergo pre-mRNA splicing to produce the same mRNA. Inhibited m⁶A sites have higher m⁶A enhancers and lower m⁶A 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. m⁶A is majorly responsible for why mRNAs with more exons be more stable. Exon junction complex (EJC) only partially contributes to this exon-intron boundary m⁶A inhibition in some short internal exons, highlighting additional factors yet to be identified.