Abstract
Internal bases in mRNA can be subjected to modifications that influence the fate of mRNA in cells. One of the most prevalent modified bases is found at the 5' end of mRNA, at the first encoded nucleotide adjacent to the 7-methylguanosine cap. Here we show that this nucleotide, N-6,2'-O-dimethyladenosine (m(6)A(m)), is a reversible modification that influences cellular mRNA fate. Using a transcriptome-wide map of m(6)A(m) we find that m(6)A(m)-initiated transcripts are markedly more stable than mRNAs that begin with other nucleotides. We show that the enhanced stability of m(6)A(m)-initiated transcripts is due to resistance to the mRNA-decapping enzyme DCP2. Moreover, we find that m(6)A(m) is selectively demethylated by fat mass and obesity-associated protein (FTO). FTO preferentially demethylates m(6)A(m) rather than N-6-methyladenosine (m(6)A), and reduces the stability of m(6)A(m) mRNAs. Together, these findings show that the methylation status of m(6)A(m) in the 5' cap is a dynamic and reversible epitranscriptomic modification that determines mRNA stability.