Hepatocyte nuclear factor-1ß regulates Wnt signaling through genome-wide competition with ß-catenin/lymphoid enhancer binding factor

Hepatocyte nuclear factor-1ß (HNF-1ß) is a tissue-specific transcription factor that is essential for normal kidney development and renal tubular function. Mutations of HNF-1ß produce cystic kidney disease, a phenotype associated with deregulation of canonical (ß-catenin-dependent) Wnt signaling. Here, we show that ablation of HNF-1ß in mIMCD3 renal epithelial cells produces hyperresponsiveness to Wnt ligands and increases expression of Wnt target genes, including Axin2, Ccdc80, and Rnf43. Levels of ß-catenin and expression of Wnt target genes are also increased in HNF-1ß mutant mouse kidneys. Genome-wide ChIP-seq in wild-type and mutant cells showed that ablation of HNF-1ß increases by five-fold the number of sites on chromatin that are occupied by ß-catenin. Remarkably, 50% of the sites that are occupied by ß-catenin in HNF-1ß mutant cells colocalize with HNF-1ß binding sites in wild-type cells, indicating widespread reciprocal binding. We found that the Wnt target genes Ccdc80 and Rnf43 contain a novel composite DNA element comprising a ß-catenin/lymphoid enhancer binding factor (LEF) site overlapping with an HNF-1ß half-site. HNF-1ß directly competes with the binding of ß-catenin/LEF complexes to this element and thereby inhibits ß-catenin-dependent transcription. Collectively, these studies reveal a novel mechanism whereby a transcription factor constrains canonical Wnt signaling through direct inhibition of ß-catenin/LEF chromatin binding. Overall design: RNA-seq and ß-catenin ChIP-seq of HNF-1ß-deficient and WT mIMCD3 cell lines treated with Mock and Wnt3a.