Fig. 4

CHST11 was identified as a downstream target of KIAA1429-mediated m6A modification on DLBCL. A A colorimetric quantification assay was used to detect the m6A levels of total RNA in OCI-LY1 and U2932 cells with KIAA1429 knockdown or overexpression. Triplicate data are presented as mean ± SD. ***p < 0.001; ****p < 0.0001. B HOMER with MeRIP-seq identified the top consensus motif of m6A peaks in OCI-LY1 cells with or without knockdown of KIAA1429. C, D The percentage of total m6A peak distribution in the specified regions was determined in cells with control and KIAA1429 knockdown. E The number of m6A peaks in control and KIAA1429-deficient cells was determined by MeRIP-seq. F The number of m6A-modified genes was revealed by MeRIP-seq, where at least one common m6A was present in the common m6A genes, whereas unique m6A genes did not contain common m6A peaks. G Venn diagram exhibiting overlap among differentially expressed genes (DEGs) from MeRIP-seq and RNA-seq and genes associated with KIAA1429 from TCGA and GEO databases. H Pearson correlations between expression of KIAA1429 and the top three genes. I RT-qPCR was used to detect the mRNA levels of the top three genes in cells with or without KIAA1429 knockdown. Results are expressed as mean ± SD from three independent experiments. *p < 0.05; **p < 0.01; ***p < 0.001. J A diminished level of CHST11 in DLBCL cells was found by RT-qPCR, compared with normal B cells. Statistical analyses are based on at least three independent experiments with mean ± SD. *p < 0.05. K The protein expression of KIAA1429 and CHST11 was negatively correlated as confirmed by western blotting. L RIP-qPCR showed direct binding between KIAA1429 and CHST11 mRNA in DLBCL cells. Data are represented as mean ± SD from three independent experiments. ***p < 0.001; ****p < 0.0001. M In vitro binding of CHST11 probes with KIAA1429 protein was demonstrated by RNA pulldown followed by western blotting