A global transcriptional co-activator, the SNF/SWI complex, has been characterized as a chromatin remodeling factor that enhances accessibility of the transcriptional machinery to DNA within a repressive chromatin structure. On the other hand, mutations in some human SNF/SWI complex components have been linked to tumor formation. We show here that SYT, a partner protein generating the synovial sarcoma fusion protein SYT-SSX, associates with native human SNF/SWI complexes. The SYT protein has a unique QPGY domain, which is also present in the largest subunits, p250 and the newly identified homolog p250R, of the corresponding SNF/SWI complexes. The C-terminal region (amino acids 310 -387) of SSX1, comprising the SSX1 portion of the SYT-SSX1 fusion protein, binds strongly to core histones and oligonucleosomes in vitro and directs nuclear localization of a green fluorescence protein fusion protein. Experiments with serial C-terminal deletion mutants of SSX1 indicate that these properties map to a common region and also correlate with the previously demonstrated anchorage-independent colony formation activity of SYT-SSX in Rat 3Y1 cells. These data suggest that SYT-SSX interferes with the function of either the SNF/SWI complexes or another SYT-interacting co-activator, p300, by changing their targeted localization or by directly inhibiting their chromatin remodeling activities.The chromatin structure of active eukaryotic genes is subject to dynamic change by chromatin modifiers such as ATP-dependent chromatin remodeling factors (reviewed in Refs. 1-5). Homologs of a yeast prototype ATP-dependent remodeling complex, SNF/SWI, appear to be widely present in eukaryotes from yeast to humans (6 -8). Functions of the subunits of the SNF/ SWI complexes (9, 10) were first demonstrated by genetic studies in Saccharomyces cerevisiae, which showed that SWI1/ ADR6, SWI2/SNF2, SWI3, and SNF5 are required for the expression of a set of genes that include the HO, GAL1, SUC2, and ADH2 genes (11-13). In Drosophila melanogaster, the SWI2/SNF2 homolog brm was originally identified as a suppressor of Polycomb mutations (14). The Drosophila complex has been isolated, and some of the subunits have been characterized (15, 16), revealing that the SNF/SWI complexes are highly conserved in subunit composition and in primary structure among yeast, fruit fly, and human. A number of studies have described various biochemical properties of the human and yeast SNF/SWI complexes, as well as other ATP-dependent chromatin remodeling complexes (reviewed in Refs. 1-3, 17). For instance the SNF/SWI complexes are recruited by transcriptional activators to nucleosomal templates (18 -23), perturb nucleosome positioning, and facilitate binding of activator proteins to nucleosomes (24 -26). Mechanisms for this perturbation have been proposed to involve interconversion between two different nucleosomal states (27), sliding of histone octamers (28) or a change of DNA topology (29, 30).The human complexes are composed of at least nine subunits that include appar...