Fig. 1: HNF4 is the top transcription factor candidate for regulating brush border genes.

a The brush border is a common feature of the intestine, kidney, and yolk sac. b Venn diagram shows that most of the brush border genes are commonly expressed in the intestine (RNA-seq FPKM > 1), kidney (RNA-seq FPKM > 1), and yolk sac (RNA-seq RPKM > 1, PRJEB18767). c Examples of brush border gene expression in the intestine, kidney, and yolk sac. d Strategy to identify transcription factors controlling brush border genes. TSSs: transcription start sites. e Accessible chromatin regions of brush border genes (±50 kb of TSSs, enhancers) were profiled by DNase-seq data in the intestine and kidney (GSE57919 and GSE51336, n = 2). k-means = 3 was used to group regions with strong DNase-seq signals. f Average signal of DNase-seq in accessible enhancer chromatin regions of brush border genes (n = 2). g HOMER motif analysis of accessible chromatin regions of brush border genes (see full list in Supplementary Data 2, MACS P ≤ 10⁻⁵, enhancer sites). Statistical tests were embedded in the MACS and HOMER packages. h RNA transcript levels of top transcription factors identified from HOMER motif analysis in the intestine, kidney, and yolk sac (RNA-seq mean FPKM or RPKM values) indicate that HNF4 is a top candidate regulator of brush border genes. i Immunofluorescence co-staining of HNF4A and brush border marker (n = 3 biologically independent mice) in the intestine (HNF4A/β-actin), kidney (HNF4A/ABCG2), and yolk sac (HNF4A/β-actin).