Decoding m⁶Am by simultaneous transcription-start mapping and methylation quantification

N ⁶,2'-O-dimethyladenosine (m⁶Am) is a modified nucleotide located at the first transcribed position in mRNA and snRNA that is essential for diverse physiological processes. m⁶Am mapping methods assume each gene uses a single start nucleotide. However, gene transcription usually involves multiple start sites, generating numerous 5' isoforms. Thus, gene levels annotations cannot capture the diversity of m⁶Am modification in the transcriptome. Here we describe CROWN-seq, which simultaneously identifies transcription-start nucleotides and quantifies m⁶Am stoichiometry for each 5' isoform that initiates with adenosine. Using CROWN-seq, we map the m⁶Am landscape in nine human cell lines. Our findings reveal that m⁶Am is nearly always a high stoichiometry modification, with only a small subset of cellular mRNAs showing lower m⁶Am stoichiometry. We find that m⁶Am is associated with increased transcript expression and provide evidence that m⁶Am may be linked to transcription initiation associated with specific promoter sequences and initiation mechanisms. These data suggest a potential new function for m⁶Am in influencing transcription.