Fig. 1. m⁶A methylome and diverse 3′UTR in SARS-CoV-2.

a Integrative Genomics Viewer (IGV) tracks displaying read distributions from m⁶A MeRIP-seq (upper panel) and RNA-seq (lower panel) along SARS-CoV-2 positive-sense RNA. The green rectangles at the bottom depict the positions of identified m⁶A peaks. b Pie chart showing the fraction of m⁶A peaks in different segments along SARS-CoV-2 RNA genome. c Line chart revealing m⁶A peak numbers per 1 kb for each segment along SARS-CoV-2 RNA genome by normalizing with its length, respectively. The diamonds represent UTRs and dots represent CDS regions along complete SARS-CoV-2 genomic RNA. d Pie chart depicting the proportion of m⁶A peaks containing RRACH (yellow) or not (blue). e Histogram showing the frequency of RRACH peak number in 1000 simulated peak pools of SARS-CoV-2 genome. f Pie chart showing proportion of reads annotated as Chlorocebus sabaeus mRNA (green), ncRNA (yellow), and SARS-CoV-2 RNA (blue). g IGV tracks showing read distribution from RNA-seq along SARS-CoV-2 RNA in both control (upper panel) and METTL3-depleted Vero cells (lower panel). The read counts were normalized by ERCC for each batch, respectively. h Heatmap showing the frequency of junction-spanning reads along SARS-CoV-2 RNA genome from control (left) and METTL3-depleted Vero cells (right). The counts were aggregated into 100-nt bins for both axes. i Models present four different types of junction-spanning reads. (a) TRS-L-dependent, canonical fusion mediated by TRS-L and TRS-B; (b) Random 3′ acceptor represents noncanonical fusion mediated by TRS-L but not TRS-B; (c) Random 5′ donor represents long-distance fusion mediated by TRS-B but not TRS-L; (d) Random inner junction identified as TRS-independent spanning. j Pie chart showing the proportions of four different types of junction-spanning reads. k Scatterplot showing the relative expression levels of four different junction-spanning transcripts in control and METTL3-depleted Vero cells which were presented in different colors, respectively. The blue circle represents the spanning-junctions located in 3′UTR. l IGV tracks displaying read distribution from m⁶A MeRIP-seq along SARS-CoV-2 RNA genome in both control and METTL3 knockdown samples. The green rectangles depict the positions of m⁶A peaks identified in control samples and yellow triangles at the bottom represent peaks with significant decreased methylation level in METTL3 knockdown samples.