Fig. 2

Nanopore sequencing of HEK293 cell lines: Mettl3 KO and WT. A Direct RNA sequencing on Nanopore. B Signature detection with JACUSA2 comparing WT over KO cells. Three principal events are detected: base substitutions, insertions and deletions. All 5mers with a central A (NNANN) are considered. C Non-negative matrix factorization to identify characteristic patterns (matrix H) that are indicative of the m6A modification. D Sequence logo of miCLIP training data (2916 sites (5mers), red 3-overlap in G). E Profile of the strongest signal from the NMF pattern matrix (H, 4th row aka NMF4) across two independent Nanopore experiments. F Sequence enrichment logo for sites with Score(NMF4 >>other patterns). G: miCLIP subsets: red 3-overlap was used for NMF training, others (shown in light blue) are used for testing. H: JACUSA2 m6A predictions: total number of predicted m6A sites in green and exact overlap with miCLIP site in brown (test data, 27,355 sites). PPV = #true CLIP sites / (#true + #false predictions). xPore performance is indicated with dashed lines