N(6)-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA 
and has been linked to diverse effects on mRNA fate. Current mapping approaches 
localize m6A residues to transcript regions 100-200 nt long but cannot identify 
precise m6A positions on a transcriptome-wide level. Here we developed m6A 
individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) 
and used it to demonstrate that antibodies to m6A can induce specific mutational 
signatures at m6A residues after ultraviolet light-induced antibody-RNA 
cross-linking and reverse transcription. We found that these antibodies 
similarly induced mutational signatures at N(6),2'-O-dimethyladenosine (m6Am), a 
modification found at the first nucleotide of certain mRNAs. Using these 
signatures, we mapped m6A and m6Am at single-nucleotide resolution in human and 
mouse mRNA and identified small nucleolar RNAs (snoRNAs) as a new class of 
m6A-containing non-coding RNAs (ncRNAs).