Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily that transcriptionally regulate responsive genes by binding to the peroxisome proliferator response elements. Protein(s) interacting with PPAR isoforms (alpha, delta, and gamma) may modulate the PPAR-mediated transcriptional activation. Using a yeast two-hybrid system to screen a rat liver cDNA library, we have identified rat deoxyuridine-triphosphatase (dUTPase, EC 3.6. 1.23) as a PPARalpha-interacting protein. This cDNA encodes a polypeptide of 203 amino acids; the C-terminal 141-amino acid segment of this protein corresponds to the full-length human enzyme, which exhibits 92% identity with human dUTPase; the N-terminal extra 62-amino acid residue region is arginine-rich. In vitro binding assays indicate that rat dUTPase interacts with all three isoforms of mouse PPAR, but not with retinoid X receptor and thyroid hormone receptor. Interaction of PPARalpha with dUTPase is with the N-terminal 62-amino acid segment of rat dUTPase. Full-length rat dUTPase prevents PPAR-retinoid X receptor heterodimerization resulting in an inhibition of PPAR activity in a ligand-independent manner. Immunostaining of human kidney tsA201 cells, transiently expressing dUTPase showed that this protein is present predominantly in the cytoplasm but translocates into the nucleus with PPARalpha when PPARalpha is coexpressed with dUTPase. Northern blot hybridization shows that rat dUTPase is encoded by an abundant 1kilobase mRNA species present in all rat tissues. The identification of dUTPase as a PPAR-interacting protein suggests a possible link between tumorigenic peroxisome proliferators and the enzyme system involved in the maintenance of DNA fidelity.