Ataxin 1 (Atx1) is a foci-forming polyglutamine protein of unknown function, whose mutant form causes type 1 spinocerebellar ataxia in humans and exerts neurotoxicity in transgenic mouse and fly expressing mutant Atx1. In this study, we demonstrate that Atx1 interacts with the transcriptional corepressor SMRT (silencing mediator of retinoid and thyroid hormone receptors) and with histone deacetylase 3. Atx1 binds chromosomes and mediates transcriptional repression when tethered to DNA. Interaction with SMRT-related factors is a conserved feature of Atx1, because Atx1 also binds SMRTER, a Drosophila cognate of SMRT. Significantly, mutant Atx1 forms aggregates in Drosophila, and such mutant Atx1-mediated aggregates sequester SMRTER. Consistently, the neurodegenerative eye phenotype caused by mutant Atx1 is enhanced by a Smrter mutation and, conversely, is suppressed by a chromosomal duplication that contains the wild type Smrter gene. Together, our results suggest that Atx1 is a transcriptional factor whose mutant form exerts its deleterious effects in part by perturbing corepressor-dependent transcriptional pathways.S pinocerebellar ataxia 1 (SCA1) is a progressive neurodegenerative disease caused by glutamine repeat expansion in ataxin 1 (Atx1) (1, 2). Other than its involvement in SCA1, the exact function of Atx1 is currently unknown. SCA1 pathology is characterized by ataxia, progressive motor deterioration, and loss of Purkinje cells in the cerebellum (3). Neurodegeneration has also been observed in transgenic SCA1 mouse and in transformed SCA1 fly when human mutant (glutamine repeatexpanded) Atx1 is ectopically expressed in mouse Purkinje cells and in Drosophila eyes, respectively (4, 5). These results suggest that specific conserved pathways are perturbed by mutant Atx1.A recent genetic screen in Drosophila (5) that sought to identify modulators of the Atx1-mediated eye phenotype has identified components involved in protein folding, protein clearance, RNA processing, and transcriptional repression as potential targets for Atx1. Although the identification of heat shock response protein͞chaperone (protein folding) and of ubiquitin͞ ubiquitin conjugase (protein clearance) in this screen has verified previous findings that these proteins are linked to polyglutamine diseases (6 -10), the association that was revealed between Atx1 and several transcriptional corepressors, including Sin3 and Rpd3 (the Drosophila histone deacetylase 1), remains unexplained.We were drawn to the results from this genetic screen in part because our earlier results indicated that silencing mediator for retinoid and thyroid hormone receptors (SMRT)-related ecdysone receptor-interacting factor (SMRTER) interacts with dSin3A (11), and because a similar interacting profile has also been observed for their vertebrate counterparts, such as SMRT and vertebrate Sin3A (12). Additionally, SMRT forms nuclear foci (13, 14) that resemble those formed by Atx1 (15, 16). These observations led us to hypothesize that SMRT and SMRTER may interact with...