Fig. 5: KDM1A negatively regulates HNF4A target genes to attenuate HNF4A function. | Nature Communications

Fig. 5: KDM1A negatively regulates HNF4A target genes to attenuate HNF4A function.

From: Transposable elements-mediated recruitment of KDM1A epigenetically silences HNF4A expression to promote hepatocellular carcinoma

Fig. 5

a, b Real-time PCR experiments were performed to analyze the expression of classical HNF4A downstream genes in KDM1A knockdown (a) or SP2509-treated (b) Huh7 and HepG2 cells, n = 3 biological replicates. Significance was examined by a two-sided t-test, and mean ± SD was shown, *P < 0.05, **P < 0.01, ***P < 0.001, ***P < 0.001. c HNF4A-luciferase plasmid and Renilla plasmid (control) were transfected into Huh7 and HepG2 cells treated with SP2509. Firefly and Renilla luciferase activities were measured and the ratio was used to reflect the transcriptional activation activity of HNF4A, n = 3 biological replicates. Significance was examined by a two-sided t-test, and mean ± SD was shown. d Venn diagram showing liver-TE-related HNF4A target genes that were significantly upregulated in KDM1A knockdown and SP2509-treated cells (sh-KDM1A-1 vs sh-control, sh-KDM1A-2 vs sh-control and SP2509 vs vehicle foldchange >2, counts >3000). e IGV browser view showing the binding of KDM1A, HNF4A, HNF1A, FOXA3, and GATA4 at the transcriptional regulatory region of the MAT1A gene, and the effect of KDM1A knockdown on the histone modifications in the transcriptional regulatory region of the MAT1A gene. f Real-time PCR experiments were performed to detect the expression of MAT1A in KDM1A knockdown or SP2509-treated HepG2 cells, n = 3 biological replicates. Significance was examined by a two-sided t-test, and mean ± SD was shown. g Western blotting was performed to detect the upregulation of MAT1A in KDM1A knockdown or SP2509-treated liver cancer cells. Each experiment was repeated three times with similar results. h Left: Cartoon plot shows the upstream and downstream metabolites of the metabolic process catalyzed by MAT1A. Right: Metabolomics analysis was performed by mass spectrometry on control and SP2509-treated HepG2 cells. The Area under the peak value of metabolites related to methionine metabolism was determined using MS-DIAL software. n = 2 biological replicates, the bar plot shows the mean value. Source data are provided as a Source Data file.

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