N⁶-methyladenosine (m⁶A) is the most abundant internal modification of eukaryotic messenger RNA (mRNA) and plays critical roles in RNA biology. The function of this modification is mediated by m⁶A-selective ‘reader’ proteins of the YTH family, which incorporate m⁶A-modified mRNAs into pathways of RNA metabolism. Here, we show that the m⁶A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells. Knockdown of YTHDC1 results in an extended residence time for nuclear m⁶A-containing mRNA, with an accumulation of transcripts in the nucleus and accompanying depletion within the cytoplasm. YTHDC1 interacts with the splicing factor and nuclear export adaptor protein SRSF3, and facilitates RNA binding to both SRSF3 and NXF1. This role for YTHDC1 expands the potential utility of chemical modification of mRNA, and supports an emerging paradigm of m⁶A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.

A new transcriptome-wide method produces reliable m ⁶ A maps at single-base resolution and reveals site conservation in mammals.

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