Abstract: SA-PO0133
A Positive-Feedback Network of Upstream Cis-Regulatory Elements Governs HNF1B Expression
Session Information
- ADPKD and Cystic Kidney Disease - 3
October 24, 2026 | Location: Exhibit Hall A, Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Genetic Diseases of the Kidneys
- 1201 Genetic Diseases of the Kidneys: Cystic (Monogenic)
Authors
- Hausch, Trinity, Stony Brook Medicine, Stony Brook, New York, United States
- Diao, Ziteng, Stony Brook Medicine, Stony Brook, New York, United States
- Igarashi, Peter, Stony Brook Medicine, Stony Brook, New York, United States
- Chan, Siu Chiu, Stony Brook Medicine, Stony Brook, New York, United States
Background
Hepatocyte nuclear factor-1β (HNF-1β) is essential for kidney development and tubular epithelial function. HNF1B nephropathy is an autosomal dominant disorder that encompasses renal cysts and diabetes (RCAD), autosomal dominant tubulointerstitial disease (ADTKD), and congenital anomalies of the kidney and urinary tract (CAKUT). Despite its clinical importance, few studies have examined the molecular mechanisms that regulate HNF1B gene expression.
Methods
Rapid immunoprecipitation-mass spectrometry of endogenous proteins (RIME) was performed in mouse mIMCD3 cells to identify HNF-1β interacting proteins. ChIP-seq, CUT&RUN and HiChIP were performed to compare GATAD2A binding sites, histone H3K27 acetylation (H3K27ac) and chromosomal loops in wild-type (WT) and HNF-1β-deficient mIMCD3 cells. CRISPR/Cas9 gene editing was used to delete putative enhancers in mIMCD3 cells, and the effects on gene expression and HNF-1β protein levels were measured using RNA-seq and western blots (WB).
Results
We identified a novel interaction between HNF-1β and the nucleosome remodeling and deacetylase complex (NuRD) at a site (E3) located 54.5 kb upstream from the Hnf1b transcription start site (TSS). ChIP-seq revealed additional NuRD binding sites located 33.4 (E1) and 31.5 kb (E2) upstream from the Hnf1b TSS. CUT&RUN analysis identified peaks of histone H3K27 acetylation at E1 and E3 in WT mIMCD3 cells. Enrichment of H3K27ac at E3 was abolished in HNF-1β-deficient cells. HiChIP analysis showed chromosomal looping between E1 and the Hnf1b promoter in WT mIMCD3 cells and a novel H3K27ac-associated loop between E1 and E3 that was absent in HNF-1β-deficient cells. Deletion of E1 or E3 in mIMCD3 cells decreased HNF-1β protein levels. RNA-seq analysis showed that E1 deletion upregulated 358 genes and downregulated 773 genes compared with wild-type controls. Notably, approximately 89% of differentially expressed genes overlapped with genes dysregulated in HNF-1β-deficient cells and were enriched for HNF-1β–regulated gene programs.
Conclusion
These results support a model in which HNF-1β mediates a positive feedback loop to sustain its own transcription through recruitment of NuRD, activation of upstream enhancers, and chromosomal looping. Elucidating the mechanism of HNF1B expression may be clinically relevant, as upregulation of HNF1B mRNA may benefit patients with HNF1B nephropathy who harbor a single functional allele.
Funding
- NIDDK Support