Reversible methylation of m6Am in the 5′ cap controls mRNA stability

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, N6,2′-O-dimethyladenosine (m6Am), is a reversible modification that influences cellular mRNA fate. Using a transcriptome-wide map of m6Am we find that m6Am-initiated transcripts are markedly more stable than mRNAs that begin with other nucleotides. We show that the enhanced stability of m6Am-initiated transcripts is due to resistance to the mRNA-decapping enzyme DCP2. Moreover, we find that m6Am is selectively demethylated by fat mass and obesity-associated protein (FTO). FTO preferentially demethylates m6Am rather than N6-methyladenosine (m6A), and reduces the stability of m6Am mRNAs. Together, these findings show that the methylation status of m6Am in the 5′ cap is a dynamic and reversible epitranscriptomic modification that determines mRNA stability.

Glycogen synthase kinase-3 (GSK-3) activity regulates mRNA methylation in mouse embryonic stem cells

“…al. also provided evidence that m 6 A demethylation is mediated by Alkbh5 (48). Our m 6 A-seq data raise the possibility that Gsk-3 activity could be directly or indirectly regulating Alkbh5, in addition to FTO.…”

“…While this manuscript was in preparation, data from Jaffrey and colleagues was published showing that FTO does not specifically demethylate m 6 A RNA, but instead prefers to demethylate m 6 A m (48 6 A relied on an antibody against m 6 A, but this antibody was shown to detect both m 6 A and m 6 A m (49). In addition, while the approach we used for m 6 A-seq did not provide us with the precise locations of demethylated adenosines in RNA from Gsk-3 DKO ESCs, we nonetheless observed hundreds of mRNAs had regions largely devoid of methylated adenosines.…”

Profiling of m6A RNA modifications identified an age‐associated regulation of AGO2 mRNA stability

“…As for RNA methylation, five types of methylation have been identified including N 7 ‐methylguanine (m 7 G at the 5' cap), N 6 ‐methyl adenosine (m 6 A), N 1 ‐methyl adenosine (m 1 A), 5‐methylcytosine (m 5 C), and 2‐ O ‐methylation (2'OME). Additionally, di‐methylation occurs when a combination of two different methylations affect the same mRNA, such as when m 6 Am is observed next to the 5' cap (Mauer et al., 2016). …”

A new twist on epigenetics

“…The researchers found that mRNAs with this mark -called m 6 Am -are more stable because their caps are harder to remove 16 . "It's exciting to people that the landscape of potentially regulated messenger RNA modifications that might influence gene expression could be an order of magnitude more complex than we thought before, " Gilbert says.…”

“…Jaffrey's work 16 suggests that FTO, which He identified as an m 6 A eraser, actually targets m 6 Am. And in October, He's group reported 17 that the enzyme Xiao flagged as a 6 mA eraser on DNA actually does a better job of stripping m 1 A off a particular type of RNA.…”