m⁶A RNA methylation in mammals

Thousands of mRNAs contain modified N⁶-methyladenosine (m⁶A), but the functional significance of this RNA modification in mammals has been unknown. Zhao and colleagues now report that the putative m⁶A methyltransferase Mettl3 and the related Mettl14 protein are required for m⁶A formation in vitro and in vivo. The two proteins appear to function synergistically, interact and regulate each other's stability. Knockdown of Mettl3 and Mettl14 in mouse embryonic stem cells (mESCs) resulted in significantly decreased m⁶A levels, and genome-wide m⁶A immunoprecipitation combined with high-throughput sequencing identified >4,700 possible RNA substrates. The Mettl3- and Mettl14-knockdown cells showed similar phenotypes typical of lost self-renewal capability. Microarray and quantitative reverse-transcription PCR analyses indicated that most pluripotency factors were downregulated in the knockdown cells, whereas some developmental regulators were upregulated. Knockdown cells also showed increased RNA stability, whereas m⁶A-modified mRNAs showed accelerated decay rates. To gain insight into the underlying mechanism, the authors focused on the RNA-stabilizing protein HuR and noted an inverse correlation between HuR binding and m⁶A-modified RNA in knockdown cells. Indeed, RNA stability of an m⁶A target mRNA, but not control transcripts that were not m⁶A targets or lacked HuR-binding sites, was regulated in a HuR-dependent manner. HuR also increased RNA stability of Mettl3 or Mettl14 targets in knockdown cells by blocking microRNA targeting. Together, these data imply that the presence of m⁶A methylation in some transcripts, particularly those encoding developmental regulators, blocks HuR binding and destabilizes them, thereby maintaining the mESC ground state. (Nat. Cell Biol. doi:10.1038/ncb2902, 7 January 2014)