Fig. 6: Collapse of an HNF4A-driven gene-regulatory network enables loss of proximal tubule identity.

a Transcription factor (TF) to target gene linkage is inferred when there is high correlation between gene expression and chromatin accessibility in cis-regulatory elements (CREs) harbouring the relevant TF binding motif. b Histogram showing the number of CREs linked to each gene. c Top panel: genes down-regulated (L2FC < -0.1, adj. p-value < 0.05) in injured/inflammatory compared with healthy PT cells (rectangular box). Bottom panel: bar graph showing TFs ordered by the number of down-regulated target genes. Colour indicates the number of CREs linked to down-regulated genes harbouring respective TF motifs. d Heatmap showing the Jaccard similarity coefficient between pairs of TFs, with 1 indicating a full overlap and 0 no overlap of target genes. e Gene-regulatory network for a subset of module A TFs. CREs are shown as diamonds with darker blue colour indicating decreased accessibility. Target genes are shown as circles with darker red colour indicating stronger down-regulation. f Changes in module A (top) and module B (bottom) TF activity along the pseudotime trajectory from healthy to inflammatory PT cells (Fig. 2f). Left: expression of genes encoding TFs. Middle: accessibility score for TF-target CREs. Right: expression of TF target genes. g HNF4-α binding sites in CREs linked to TFs in module A and B. Edge width indicates the number of bound CREs and colour the mean accessibility change (negative values indicate reduced accessibility in injured/inflammatory compared with healthy PT cells). h HNF4-α motif footprint in PT cell states. i Violin plots of HNF4-α target gene expression in PT cells (dots coloured according to cell phenotypes) following ischaemia-reperfusion injury in mice (Fig. 2i). j Upper: chromatin accessibility in healthy, injured and inflammatory PT cells at the HNF4A locus with corresponding HNF4A mRNA expression (right, dot size scaled by the proportion of cells expressing the gene and coloured by the average (log-scale) expression). Middle: regions harbouring HNF4-α motifs. Lower: HNF4-α CUT&RUN signal in adult human kidney³⁰. k Sustained injury disrupts the HNF4A auto-regulatory loop, depleting HNF4A mRNA and protein leading to loss of PT identity.