Multi-Domain Integration in the Structure of the HNF4α Nuclear Receptor Complex

The hepatocyte nuclear factor 4 alpha (HNF4α, NR2A1) is a member of the nuclear receptor (NR) family of transcription factors that use conserved DNA binding domains (DBDs) and ligand binding domains (LBDs)(1,2). HNF4α is the most abundant DNA-binding protein in the liver, where some 40% of the actively transcribed genes have a HNF4α response element (1,3,4). These regulated genes are largely involved in the hepatic gluconeogenic program and lipid metabolism(3,5,6). In the pancreas too, HNF4α is a master regulator controlling an estimated 11% of islet genes(7). HNF4α protein mutations are linked to Maturity Onset of Diabetes in Young 1 (MODY1) and hyperinsulinemic hypoglycemia (HH)(8–11). Prior structural analyses of NRs, while productive with individual domains, have lagged in revealing the connectivity patterns of NR domains. Here, we describe the 2.9 Å crystal structure of the multi-domain HNF4α homodimer bound to its DNA response element and coactivator-derived peptides. A convergence zone connects multiple receptor domains in an asymmetric fashion joining distinct elements from each monomer. An arginine target of PRMT1 methylation protrudes directly into this convergence zone and sustains its integrity. A serine target of protein kinase C is also responsible for maintaining domain-domain interactions. These post-translational modifications manifest into changes in DNA binding by communicating through the tightly connected surfaces of the quaternary fold. We find that some MODY1 mutations, positioned on the LBD and hinge regions of the receptor, compromise DNA binding at a distance by communicating through the inter-junctional surfaces of the complex. The overall domain representation of the HNF4α homodimer is different from that of the PPARγ-RXRα heterodimer, even when both NR complexes are assembled on the same DNA element. Our findings suggest that unique quaternary folds and inter-domain connections in NRs could be exploited by small-molecule allosteric modulators that impact distal functions in these polypeptides.