The SWI/SNF Subunit INI1 Contains an N-Terminal Winged Helix DNA Binding Domain that Is a Target for Mutations in Schwannomatosis

SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation. Mutations in SWI/SNF subunits are among the most frequent gene alterations in cancer. The INI1/hSNF5/SMARCB1 subunit is mutated in both malignant rhabdoid tumor, a highly aggressive childhood cancer, and schwannomatosis, a tumor-predisposing syndrome characterized by mostly benign tumors of the CNS. Here, we show that mutations in INI1 that cause schwannomatosis target a hitherto unidentified N-terminal winged helix DNA binding domain that is also present in the BAF45a/PHF10 subunit of the SWI/SNF complex. The domain is structurally related to the SKI/SNO/DAC domain, which is found in a number of metazoan chromatin-associated proteins. •INI1 and its metazoan homologs contain a variant winged helix DNA binding domain•A homologous domain is present in the BAF45a/PHF10 subunit of the SWI/SNF complex•Structurally related domains are found in other metazoan chromatin-associated proteins•INI1 mutations that cause schwannomatosis map to the winged helix domain Allen et al. show that the INI1/hSNF5/SMARCB1 subunit of the human SWI/SNF chromatin-remodeling complex contains a variant winged helix DNA binding domain. Mutations in INI1 that cause the tumor-predisposing syndrome schwannomatosis perturb the fold or disrupt the function of this domain.