Fig. 4: Transcriptional inactivation of TCF7L2 eliminates zone 3 gene expression.
Multiomics analysis was performed on nuclei isolated from the livers of TCF7L2LoxP/LoxP (n = 3) and Hep-TCF7L2ΔDBD (n = 3) mice. A Single nuclei RNA-Seq (snRNA-Seq), (B) single nuclei ATAC-Seq (snATAC-Seq), and (C) integrated weighted nearest neighbor (WNN) are shown. In Hep-TCF7L2ΔDBD mice, nuclei corresponding to zone 3 were largely absent and instead clustered with zone 2 nuclei. D Heatmap of gene expression following trajectory analysis reveals the clear absence of zone 3 gene expression in Hep-TCF7L2ΔDBD. The color gradient above the heatmap is for visual purposes only. E Differential expression analysis confirms that the loss of TCF7L2 transcription had minimal impact on zone 1 and 2 genes, but significantly impacted the expression of genes in zone 3 nuclei. For this DEG analysis, TCF7L2 mutant zone 3 nuclei were identified based on their clustering relative to zone 3 nuclei in the control mice. F In snATAC-Seq analysis, accessibility of the TCF7L2 binding motif was disrupted in zone 3 nuclei isolated from Hep-TCF7L2ΔDBD mice. Mutant zones 2 and 3 nuclei were combined for statistical comparison with respective control nuclei, as detailed in the text. G TCF7L2 loss of function alters the motif accessibility of several transcription factors that may contribute to the maintenance of metabolic zonation. Heatmap of chromVAR regression scores of motifs that were associated with the hepatocyte trajectory and displayed significant differences in accessibility between zones. H Analysis of snATAC-Seq data using Signac highlights the reduction of transcription factor (TF) motif accessibility in zones 2 and zones 3. A heatmap of fold enrichment for motif binding sites within sets of differentially less accessible chromatin regions between TCF7L2 and control nuclei in each hepatocyte zone. Source data are provided as a Source Data file. Single nuclei data are available for download at GEO (accession: GSE239480).
