Fig. 2: m⁶Am-seq uncovers the high-confidence m⁶Am and 5′-UTR m⁶A methylation in the human transcriptome.

Motif analysis of m⁶Am peaks (a) and 5′-UTR m⁶A peaks (b) identified by m⁶Am-seq. c Representative views of typical m⁶Am peaks and 5′-UTR m⁶A peaks on mRNA. The methylation peak in the 5′-UTR of PAX6 was lost in “FTO (+) m⁶A-IP” samples, suggesting a demethylase-sensitive m⁶Am modification (top); the methylation peak in the 5′-UTR of SQLE retained well in “FTO (+) m⁶A-IP” samples, suggesting a demethylase-insensitive m⁶A modification (middle); while multiple isoforms of ATF5 were differentially marked by m⁶Am and 5′-UTR m⁶A (bottom). Pink and blue background colors denote m⁶Am and m⁶A signals, respectively. d Venn diagram showing the overlap between m⁶Am peaks identified directly by m⁶Am-seq and m⁶Am peaks identified indirectly by m⁶A IP using PCIF1-KO samples. e Boxplot showing that the peak intensity of m⁶Am (red, n = 1652), but not that of m⁶A (blue, n = 1307), was significantly reduced upon PCIF1 depletion. Statistical significance of the difference was determined by unpaired two-sided Mann–Whitney U-test. ****P < 2.2e⁻¹⁶. Boxes represent 25th–75th percentile (line at median) with whiskers at 1.5*IQR. Source data are provided as a Source Data file.