Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase

N-6-methyladenosine (m(6)A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m(6)A, N-6, 2'-O-dimethyladenosine (m(6)Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the serine-5-phosphorylated carboxyl-terminal domain of RNA polymerase II, as a cap-specific adenosine methyltransferase (CAPAM) responsible for N-6-methylation of m(6)Am. The crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m(6)A formation. A transcriptome-wide analysis revealed that N-6-methylation of m(6)Am promotes the translation of capped mRNAs. Thus, a cap-specific m(6)A writer promotes translation of mRNAs starting from m(6)Am.