Fig. 3

Characterization of m6A modification and identification of KIAA1429 downstream target. a and b Relative m6A levels on poly-A selected RNA in indicated SK-Hep1 and HCCLM3 cells were assessed by the EpiQuik m6A RNA Methylation Quantification Kit (Colorimetric). c Top sequence motif identified from MeRIP-seq peaks in control and KIAA1429-depleted cells. d Volcano plot of altered m6A peaks identified in MeRIP-seq in control and KIAA1429-depleted cells. e Distribution of reduced m6A peaks generated by KIAA1429 inhibition across all mRNAs. f Schematic of the selection for the direct downstream target of KIAA1429. g RIP-seq of the enrichment of candidate mRNA transcripts on KIAA1429 relative to IgG. h RNA-seq of the fold change of candidate mRNA transcripts caused by KIAA1429 depletion. i GATA3 expression in 70 pairs of HCC tissues and adjacent normal tissues from WCH dataset by using qPCR. j Scatter plots of KIAA1429 versus GATA3 expression in WCH data repository. Pearson correlation coefficients (r) and P values are shown. k-l GATA3 expression in SK-Hep1 and HCCLM3 cells with stable KIAA1429 knockdown by using qPCR. m and n GATA3 expression in SK-Hep1 and HCCLM3 cells with transient KIAA1429 knockdown by using qPCR. o and p Western blot analysis of GATA3 expression in SK-Hep1 and HCCLM3 cells with stable and transient KIAA1429 knockdown. Data are presented as mean ± SEM. **P < 0.01, ***P < 0.001