Fig. 4

Transcriptome-wide identification of m⁶A targets that regulate tumorigenesis. a Volcano plots showing m⁶A enrichment of genes in normal and tumor cells. b GO enrichment map of genes with specific enriched m⁶A peaks in control normal cells. c Schematic of m⁶A modification downstream analysis. In normal cells, RNA-seq detected 5714 genes with differential expression in which 3506 genes were upregulated and 2208 genes were downregulated. m⁶A-miCLIP-seq showed that 2826 genes were differentially methylated. In normal cells, 2357 genes were up-methylated, and 469 genes were down-methylated. Protein quantification analysis revealed 1003 genes with differential protein levels in normal cells: 478 genes had upregulated protein levels, and 525 genes had downregulated protein levels. In the group of genes with higher m⁶A levels, 254 genes were upregulated, and 159 genes were downregulated. However, 2241 genes with m⁶A methylation levels showed no expression change in normal cells. Finally, we found that 237 genes also had differential m⁶A levels with differential protein levels. The cutoffs used for differentially expressed genes, differential methylation levels and genes with differential protein levels were FC < − 1.5 or FC > 1.5 and p < 0.05. FC: fold change, p: p-value. d Representative GO biological process categories enriched in genes with significant differences in m⁶A enrichment and protein content but not gene expression. e Volcano plots showing the m⁶A enrichment and protein content of genes in normal cells compared to tumor cells. f IGV tracks displaying the miCLIP-seq reads coverage of HINT2 in normal and tumor cells