Fig. 3: Prioritization and functional validation of HNF4A-bound beta cell targets.

a IGV tracks showing HNF4A ChIP-Seq peaks in selected loci in D35 βLCs, EndoC-βH1 cells, and human islets. The scale used to visualize peaks in IGV is indicated on the right side of each track. The chromosomal location near the peak region is indicated. b Gene expression analysis of selected target genes in EndoC-βH1 cells with HNF4A siRNA-mediated knockdown (n = 5). * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001 relative to si-NT control, based on unpaired two-tailed Students’ t test. c Gene expression analysis of selected target genes in EndoC-βH1 cells overexpressing GFP (empty vector), HNF4A WT, T139I variant, or MODY1 I271fs variant constructs (n = 4). * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001 relative to GFP control; $ indicates p < 0.05 relative to WT, based on one-way ANOVA with Tukey’s post-hoc test. d Transactivation activities at selected target promoters in EndoC-βH1 cells using luciferase reporter assays (n = 3 for ACY3/HAAO/USH1C; n = 4 for VIL1). * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001 relative to Empty si-HNF4A control; $ indicates p < 0.01 relative to WT, based on one-way ANOVA with Tukey’s post-hoc test. e Glucose-stimulated insulin secretion (GSIS) in EndoC-βH1 cells with siRNA-mediated KD of selected target genes (n = 4). * indicates p < 0.05 relative to si-NT control, based on two-way ANOVA with Dunnett’s multiple comparisons test. f Insulin secreted as a percentage of total insulin in EndoC-βH1 cells with siRNA-mediated KD of selected target genes, at 16.7 mM glucose stimulation (n = 4). P value indicated is based on paired two-tailed Students’ t test. Data are presented as mean ± SD. Each data point represents one independent experiment. Source data and exact P values are provided in the Source Data file.