Fig. 3. METTL3-mediated m⁶A upregulation on APC mRNA.

a m⁶A content of total RNA in KYSE180 cells with or without METTL3 depletion was determined. Data represent the means ± SD of triplicate samples. **p = 0.0094 based on two-tailed Student’s t-test. b The most frequent m⁶A motifs detected by DREME software in MeRIP-seq of KYSE180 cells are shown. c MeRIP-seq of KYSE180 cells with or without METTL3 depletion was conducted. The proportions of m⁶A peak distribution in the 5′-untranslated region (5′-UTR), start codon, coding region (CDS), stop codon and the 3′-untranslated region (3′-UTR) across the entire set of mRNA transcripts were calculated. d The genes with diminished m⁶A peaks identified by MeRIP-seq (1101 genes, fold-change > 2) and the genes with upregulated or downregulated mRNA expression (2973 genes, fold-change > 2) identified by RNA-seq in KYSE180 with or without METTL3 depletion were analysed (93 genes overlapped). e The m⁶A peak visualization of m⁶A-seq in APC transcripts in KYSE180 cells with or without METTL3 depletion is shown. The m⁶A peaks are in the last exon of APC. f The MeRIP-Seq peak in KYSE180 regulated by METTL3 depletion and miCLIP peaks in other types of cancer cells from the Gene Expression Omnibus were aligned. The three methylated adenosine bases were denoted with red colour. g, h Methylated RNA in KYSE180 cells with or without METTL3 depletion (g), METTL3 expression or METTL3 and METTL14 shRNA expression (h) was immunoprecipitated with an m⁶A antibody followed by qPCR analyses with primers against APC mRNA. Data represent means ± SD of triplicate samples. g ***p = 3.84E − 05 (left), 8.99E − 05 (right); **p = 0.0012 (middle). h **p = 0.0019. Two-tailed t-test; ns, not significant. i RIP analyses of KYSE180 and KYSE450 cells were performed with an anti-METTL3 antibody followed by qPCR analyses with primers against APC mRNA. Data represent means ± SD of triplicate samples. ***p = 2.50E − 05 (left), 1.08E − 05 (right). Two-tailed t-test. Source data are provided as a Source Data file.