Transcriptome-wide profiling and quantification of N-methyladenosine by enzyme-assisted adenosine deamination.

N-methyladenosine (mA), the most abundant internal messenger RNA modification in higher eukaryotes, serves myriad roles in regulating cellular processes. Functional dissection of mA is, however, hampered in part by the lack of high-resolution and quantitative detection methods. Here we present evolved TadA-assisted N-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology that detects and quantifies mA by global adenosine deamination. With eTAM-seq, we analyze the transcriptome-wide distribution of mA in HeLa and mouse embryonic stem cells. The enzymatic deamination route employed by eTAM-seq preserves RNA integrity, facilitating mA detection from limited input samples. In addition to transcriptome-wide mA profiling, we demonstrate site-specific, deep-sequencing-free mA quantification with as few as ten cells, an input demand orders of magnitude lower than existing quantitative profiling methods. We envision that eTAM-seq will enable researchers to not only survey the mA landscape at unprecedented resolution, but also detect mA at user-specified loci with a simple workflow.