Actin-related protein (Arp) is found in many chromatin remodeling and histone acetyltransferase complexes. We previously identified ArpNalpha as an isoform of ArpNbeta/BAF53, which is included in mammalian SWI/SNF chromatin remodeling complex, and showed that ArpNalpha is a potential component of the complex. Although it has a structure highly similar to ArpNbeta/BAF53, ArpNalpha is expressed exclusively in brain and in neural differentiated embryonal carcinoma cells. Since ArpNa possesses a region that shows low similarity to ArpNbeta/BAF53, we hypothesized that proteins interacting with this region contribute to the ArpNalpha-specific function in brain. Here we showed that ArpNalpha, but not ArpNbeta/BAF53, interacts with the transcriptional co-repressor CtBP (C-terminal binding protein). Transactivation by the SWI/SNF complex and glucocorticoid receptor was repressed by the CtBP in the presence of ArpNalpha. These findings suggest that SWI/SNF complex containing ArpNalpha might regulate certain genes involved in brain development and/or its function differently from SWI/SNF complex containing ArpNbeta/BAF53. (C) 2003 Elsevier Science (USA). All rights reserved.