Hepatocyte nuclear factor 4 (HNF-4), a highly conserved member of the steroid hormone receptor superfamily critical for development and liver-specific gene expression, is very similar to another superfamily member, retinoid X receptor ␣ (RXR␣), in overall amino acid sequence and DNA binding specificity. Since RXR␣ is known to heterodimerize with many other nuclear receptors, the formation of heterodimers between HNF-4 and RXR␣ was examined. With the electrophoretic mobility shift assay, coimmunoprecipitation, and transient transfection assays, it is shown that, unlike other nuclear receptors, HNF-4 does not form heterodimers with RXR␣ either in the presence or in the absence of DNA. We also show that in vitro-translated HNF-4 does not form heterodimeric complexes on DNA with a number of other receptors, including RXR, RXR␥, retinoic acid receptor ␣, or thyroid hormone receptor ␣. To investigate the hypothesis that the lack of heterodimerization between HNF-4 and RXR␣ is due to a strong homodimerization activity of HNF-4, glycerol gradient sedimentation and kinetic analysis were used to show that HNF-4 is in fact a stable homodimer in solution. Finally, immunohistochemistry is used to show that the HNF-4 protein is found exclusively in the nuclei in both HepG2 cells, which express endogenous HNF-4, and transfected COS cells, which overexpress HNF-4. These findings lead us to propose that HNF-4 defines a new subclass of nuclear receptors which reside primarily in the nucleus and which bind DNA and regulate transcription as homodimers.Hepatocyte nuclear factor 4 (HNF-4) is a positive-acting transcription factor which is expressed very early in embryo development and is essential to liver development and function (reviewed in references 84 and 85). Mouse HNF-4 mRNA appears in the primary endoderm of implanting blastocysts at embryonic day 4.5 and in the liver and gut primordia at day 8.5 (20), while mice deficient in HNF-4 do not survive past day 9 postcoitus (12). HNF-4 has also been proposed to be responsible for the final commitment for cells to differentiate into hepatocytes (68). In adult rodents, HNF-4 is located primarily in the liver, kidney, and intestine, and in insects HNF-4 is found in the equivalent tissues (86, 95). HNF-4 is known to activate a wide variety of essential genes, including those involved in cholesterol, fatty acid, and glucose metabolism; blood coagulation; detoxification mechanisms; hepatitis B virus infections; and liver differentiation (reviewed in references 84 and 85).HNF-4 is a member of the superfamily of ligand-dependent transcription factors, which includes the steroid hormone receptors, thyroid hormone receptor (TR), vitamin A receptor, and vitamin D receptor (VDR), as well as a large number of receptors for which ligands have not yet been identified, the so-called orphan receptors (reviewed in references 56, 72, 73, and 88). All receptors are characterized by two conserved domains: the zinc finger region, which mediates DNA binding, and a large hydrophobic domain which mediate...