Fig. 3: Detection of m⁶A sites using MePMe-seq.

a Distribution of all modified nucleotides identified in MePMe-seq. b Overlap of m⁶A sites identified in n = 2 independent experiments (% calculated from rep2 to rep1). c Integrative genomics viewer (IGV) browser coverage tracks of MePMe-seq data for the indicated AHNAK and YTHDF2 mRNAs from cells labeled with PSH (purple) or methionine as control (gray). Green bars indicate terminations identified by JACUSA2 applying high stringency filtering. Numbers (%) for calculated arrest rate at indicated positions are shown. Arrow indicates orientation of coding strand. d Frequency of m⁶A sites per transcript. e Frequency of distance between neighboring m⁶A positions located on the same transcript. Cutoff at 1000 nt (for cutoff at 5000 nt see Supplementary Fig. 14a). f Metatranscript analysis showing a density plot of the distribution of prop⁶A sites detected by MePMe-seq. g Consensus motif for sequences surrounding identified m⁶A (HS filtering) for all 5-mers (all), if DRACH sequences are excluded (non-DRACH) or if NRACN sequences are excluded (non-NRACN). Representative example of n = 2 biologically independent samples is shown (2nd replicate: Supplementary Fig. 14b). h Sequence motifs surrounding identified m⁶A sites (HS filtering), sorted by consensus motif DRACH, NRACN or non-NRACN, respectively. Arrow indicates ACAGA-motif, which is part of METTL16 motif. i Overlap of all 4502 m⁶A sites identified in MePMe-seq with sites identified by MeRIP, GLORI, m⁶A-SAC-seq, SEAL, miCLIP, m⁶A CLIP, PA-m⁶A-CLIP, eTAM-seq, m⁶A-seq improved (imp.), m⁶A-REF-seq, DART-seq and m⁶A-label-seq^64,81,82,91.