In this study, we describe the characterization of a novel nuclear protein, referred to as RAP80. The RAP80 cDNA was cloned from a human testis cDNA library and encodes a 719-amino acid protein containing two potential CX 2 CX 11 HX 3 C-type zinc finger motifs at its carboxylterminal region. Analysis of its genomic structure revealed that the RAP80 gene covers more than 90 kb and consists of 15 exons and 14 introns. Fluorescence in situ hybridization mapped the RAP80 gene to human chromosome 5q35. RAP80 mRNA is expressed in many human tissues, but its expression is particularly high in testis. In situ hybridization showed that RAP80 is highly expressed in germ cells of mouse testis but is not differentially regulated during spermatogenesis. Confocal microscopy showed that RAP80 is localized to the nucleus, where it is distributed in a speckled pattern. Deletion analysis showed that a bipartite nuclear localization signal at the amino terminus is important in mediating nuclear transport of RAP80. Monohybrid analysis showed that RAP80 might function as an active repressor of transcription. Mammalian two-hybrid analysis demonstrated that RAP80 was able to interact with the retinoid-related testis-associated receptor (RTR), an orphan receptor that has been implicated in the control of embryonic development and spermatogenesis. Pulldown analysis showed that RAP80 and RTR physically interact in vitro. Deletion and point mutation analyses revealed that part of the hinge domain of RTR is required for this interaction. RAP80 is able to inhibit the interaction of RTR with the co-repressor N-CoR likely by competing with N-CoR for RTR binding. Our results suggest that RAP80 may be functioning as a modulator of RTR signaling.The nuclear receptor superfamily is composed of a large number of ligand-dependent transcription factors that include nuclear orphan receptors for which a ligand has not yet been identified (1-4). Nuclear receptors share a common domain structure that includes an amino-terminal domain, a DNAbinding domain (DBD), 1 hinge domain, and a ligand-binding domain (LBD). These domains are involved in the recognition of specific DNA response elements, receptor dimerization, nuclear localization, and ligand binding and contain repressor and transactivation functions. Repression and activation of transcription by nuclear receptors are mediated through interactions with co-repressor and co-activators, respectively. Nuclear receptors have been demonstrated to regulate many physiological processes, including embryonic development and cell growth and differentiation and have been implicated in a number of human diseases (5-8). Less, however, is known about the role of many nuclear orphan receptors, including the retinoidrelated, testis-associated receptor (RTR), also referred to as germ cell nuclear factor (9, 10). The orphan receptor RTR (named NR6A1 by the Nuclear Receptor Nomenclature Committee) has been cloned from several species, including mouse (9, 10), human (11-14), zebrafish (15), and Xenopus laevis (16). Duri...