Regulation of Kidney-Specific Gene Expression

ABSTRACT The purpose of this MERIT renewal is to continue our studies on hepatocyte nuclear factor-1β (HNF-1β) and its roles in kidney-specific gene expression and cystic kidney diseases. HNF-1β is a DNA-binding transcription factor that regulates tissue-specific gene expression in the kidney and other epithelial organs. Mutations of HNF- 1β produce congenital anomalies of the kidney and urinary tract, cystic kidney disease, autosomal dominant tubulointerstitial kidney disease, and inherited tubulopathies. To unravel the pathogenesis of these disorders, we have produced HNF-1β mutant mice that develop phenotypes similar to those seen in affected humans. Analysis of the mutant mice has revealed that HNF-1β plays a central role in the expression of polycystic kidney disease genes, such as PKD2 and PKHD1. During the last project period, we used genome-wide ChIP-seq and RNA-seq to identify transcriptional networks that are directly regulated by HNF-1β. Together with new mutant mouse models, these studies uncovered novel roles of HNF-1β in the regulation of Wnt signaling, cAMP signaling, lipid metabolism, urinary concentration, and expression of noncoding RNAs. Preliminary studies using mass spectrometry revealed that HNF-1β interacts with proteins involved in chromatin remodeling, histone modification, and transcription elongation. In the next project period we will extend this work to further unravel the functions of HNF-1β in the kidney. Specific Aim 1 will use biochemical studies to unravel the molecular mechanisms whereby HNF-1β represses Wnt pathway genes. We will test the hypothesis that HNF-1β forms repressive chromatin loops that exert long-range effects on histone modification, chromatin remodeling, and transcription elongation. Specific Aim 2 will apply mouse genetics to elucidate the roles of dysregulated Wnt signaling in the HNF-1β mutant phenotype. We will determine whether mutations of Wnt pathway genes that are overexpressed in HNF-1β mutant mice improve kidney function and structure. Collectively, the proposed studies will advance our understanding of gene regulation, unravel how mutations of HNF-1β produce kidney abnormalities, and identify potential therapeutic targets for HNF-1β-related cystic kidney diseases.