Comprehensive characterisation of HNF4A and HNF1A genomic targets in pancreatic beta cells and hepatic cells reveals common and tissue-specific pathways and genes

To determine the downstream regulatory network of HNF4A and HNF1A, two transcription factors that play important roles in the pancreas and liver and that are associated with diabetes, we generated a comprehensive genome-wide map of the binding targets of HNF4A and HNF1A in hiPSC-derived pancreatic and hepatic cells and relevant cell lines using ChIP-Seq and molecular validation. We report binding targets of HNF4A and HNF1A that map to both known and novel gene promoters, that are common or differentially bound across different cell types and developmental stages. Overall, the detailed characterisation of the regulatory roles of HNF4A and HNF1A in pancreatic beta cells and hepatic cells will potentially shed light on how dysregulation of these factors can contribute to altered tissue development and function, and thus pathogenesis of both monogenic diabetes and T2D. Overall design: Chromatin immunoprecipitation and sequencing (ChIP-Seq) was performed using antibodies against HNF4A and HNF1A in multiple cell types (EndoC-ßH1 cells, human islets, hiPSC-derived pancreatic progenitors, hiPSC-derived endocrine progenitors, hiPSC-derived beta-like cells, hiPSC-derived hepatoblasts and HepG2 cells). ChIP-Seq was also conducted using the antibody against FLAG in EndoC-ßH1 cells stably overexpressing FLAG-tagged HNF4A8 WT or T117I variant. Validation by ChIP-qPCR confirmed binding at selected targets.