The SWI/NF complexes bind to DSB-surrounding chromatin via interaction with γ-H2AX. (A) BRG-1 and mouse Brm (mBrm) bind to chromatin after DNA damage. NIH-3T3 cells were untreated or irradiated by 10 Gy, and after 1 h cells were collected and subjected to detergent extraction. Sequentially fractionated extracts (Fractions I–III) and pellet (Fraction IV) were subjected to immunoblottings with the antibodies against BRG-1, mBrm and Nbs1. A representative of four independent experiments is shown. (B) Time-course analysis for the chromatin binding of BRG-1 and mBrm (data not shown) after DNA damage. NIH-3T3 cells were untreated (0 Gy) or irradiated by 10 Gy, and at various time points after irradiation, cells were collected and subjected to detergent extraction chromatin retention assays as in (A). Equal protein loading was ensured by Ponceau staining (data not shown). Immunoblots for fraction III are shown. A representative of four independent experiments is shown. (C) Binding of BRG-1 and mBrm (data not shown) to chromatin increases in proportion to irradiated IR doses. NIH-3T3 cells were untreated (0 Gy) or irradiated by 2, 5, 10, 25 and 50 Gy. After 1 h, cells were collected and subjected to detergent extraction chromatin retention assays as in (A). Equal protein loading was ensured by Ponceau staining (data not shown). Immunoblots for fraction III are shown. A representative of three independent experiments is shown. (D) BRG-1 is specifically retained in the chromatin overlapping with γ-H2AX after detergent extraction. NIH-3T3 cells untreated (0 Gy) or irradiated by 5 Gy, and after 1 h, the cells were detergent fractionated in situ. Cells were then fixed and double stained with the antibodies for γ-H2AX and BRG-1 with the nuclei labeled with DAPI. The third row shows a representative staining pattern of the irradiated cells shown in the second row. (E) The phosphorylation of Flag-H2AX at Ser-139 (Flag-γ-H2AX) was analyzed using the histones extracted from 293T cells that stably express N-terminal Flag-tagged H2AX after irradiation as indicated. The size differences permitted a detection of Flag-tagged proteins and their endogenous counterparts on the same immunoblot gel using the antibodies for γ-H2AX or H2AX. The first lane is nonirradiated 293T cells harboring empty vector. (F) Flag-H2AX expressing 293T cells were examined for nuclear focus formation by double staining with the Flag and γ-H2AX antibodies 1 h after irradiation by 2 Gy. (G) 293T cells expressing an empty vector or Flag-H2AX were subjected to ChIP at 1 h after irradiation by 10 Gy. After formaldehyde crosslinking and sonication, chromatin was immunoprecipitated by anti-Flag antibodies and co-precipitation of BRG-1, hBrm and Nbs1 was analyzed by immunoblottings with the indicated antibodies.