FIGURE 3.

Transcriptome-wide RNA m⁶A methylation and expression analysis of MIA PaCa-2 stable cell line with ALKBH5 overexpression. (A) Top consensus motif of m⁶A peaks identified in empty vector (EV) or ALKBH5-overexpressing (OE) MIA PaCa-2 cells. (B) Normalized distribution of m⁶A peaks across 5′UTR, CDS, and 3′UTR of mRNAs. (C) Cumulative distribution function of log2 enrichment score of m⁶A modified sites. (D) GO term analysis of transcripts with hypo- (left panel) and hyper-methylated (right panel) m⁶A sites in OE sample versus EV sample. (E) Scatter plot representing the log₂FC of methylation (x-axis) and expression (y-axis) of each m⁶A peak in OE versus EV sample. Points with |log₂FC| > 0.58 in both differential expression and methylation analysis results are highlighted. (F) Venn diagram showing the RNAs with significant change in either methylation (|log₂FC| > 0.58 and FDR < 0.05) or expression (|log₂FC| > 0.58 and P < 0.05) in OE sample. (G) Histogram showing the fold changes in m⁶A enrichment between OE and EV samples from total RNA based m⁶A data. Dotted lines denote the threshold (|log₂FC| > 0.58) for filtering differential expression gene. (H) Scatter plot showing the distribution of fold changes in methylation (x-axis) and expression (y-axis) of each RNA in OE versus EV sample. Two RNAs with significantly decreased m⁶A methylation and increased expression level in OE sample are marked in red. Points in rectangle shape represent significant changes in methylation (|log₂FC| > 0.58 and FDR < 0.05) and expression (|log₂FC| > 0.58, P < 0.05), while the rest ones are shaped in circle.