Isolation of Nuclear Extracts for Protein Analysis

Nuclear extracts were isolated using the standard approach (73 (link), 79 (link), 80 (link)). Briefly, cells were grown to 80% confluence and then exposed to C. parvum for various times. Cells were treated with EDTA (Sigma) and washed with PBS, and the cell pellet was resuspended in 1 ml of cold buffer A (10 mM HEPES, 1.5 mM MgCl₂, 10 mM KCl, and 1 mM dithiothreitol [DTT]). Nuclear pellets were isolated from the whole-cell protein by centrifugation at 14,000 rpm for 1 min at 4°C and resuspended in cold buffer B (20 mM HEPES, 1.5 mM MgCl₂, 25% glycerol, 420 mM NaCl, 0.2 mM EDTA, and 1 mM DTT) with vigorous agitation in the cold room for 30 min. The supernatant containing nuclear proteins was collected after centrifugation at 14,000 rpm for 5 min at 4°C. Protein concentration of each nuclear extract or whole-cell lysate was determined and subsequently analyzed by Western blotting. The following antibodies were used for blotting (details in Table S1): anti-Brg1 (Santa Cruz), anti-H3K36me3 (Abcam), anti-H3K4me3 (Abcam), anti-Stat1 (Cell Signaling), anti-pStat1 (Cell Signaling), anti-Pias1 (Santa Cruz), anti-Snf5 (Santa Cruz), anti-Baf170 (Cell Signaling), anti-p50 (Abcam), anti-Elf3 (Santa Cruz), anti-Cdc42 (Fisher Scientific), anti-Actin (Sigma), and anti-Prdm1 (Cell Signaling).