For nuclear extractions, all procedures were performed on ice. Culture dishes (10-cm diameter) were washed once with 10 mM ice-cold PBS. Cells were harvested by centrifugation at 200
g for 10 minutes at 4°C. The cell pellets were washed twice with ice-cold PBS, followed by centrifugation at 200
g for 5 minutes at 4°C, and resuspended with 5 vol of Buffer A in mM: 20 HEPES, 1.5 MgCl
2, 10 KCl, 1 EDTA, 1 EGTA, 250 sucrose, 0.1 PMSF, 1 dithiothreitol (DTT), and 1× protease inhibitor cocktail, pH 7.9.
25,26 After a 10-minute incubation on ice, cells were homogenized with a minipestle. The lysates were centrifuged at 750
g for 15 minutes at 4°C; the nuclear pellets were washed twice with the same lysis buffer, resuspended in 45 μL of Buffer B in mM: 20 HEPES, 1.5 MgCl
2, 20 KCl, 0.2 EDTA, 0.5 DTT, 0.2 PMSF, 1× protease, and phosphatase inhibitor cocktail, pH 7.9, on ice for 30 minutes; and 15 μL of Buffer C in mM: 20 HEPES, 1200 KCl, 0.2 EDTA, 0.5 DTT, 0.2 PMSF, 1× protease and phosphatase inhibitor cocktail, pH 7.9, were added and mixed. The samples were placed on ice for 30 minutes and centrifuged at 15,000
g. Supernatants containing nuclear protein were transferred and stored at −80°C until analysis. Protein concentrations were determined using the Bradford method. For DNA-binding reactions, 5 μg of nuclear protein was diluted in binding buffer (10 mM Tris-HCl, 50 mM KCl, 1 mM DTT, 2.5% glycerol, 5 mM MgCl
2, 0.05% Nonidet P-40, 1 mM β-mercaptoethanol, 50 μg/mL poly[dI:dC]; pH 7.5). After a 30-minute incubation on ice, a biotin-labeled oligonucleotide probe (50 fmol) was added, and the reaction was continued for another 20 minutes. The probes were commercially available PPRE probes labeled at the 5′ end with biotin (F: 5′-CAA AAC T
AG GTC AA
A GGT CA-3′; R: 5′-TGA CCT TTG ACC TAG TTT TG-3′, the consensus sequence for PPRE was underlined) (synthesized by Shanghai Biotechnology, Inc.). The probes were heated in Tris-HCl buffer at 85°C for 10 minutes and then sat in room temperature for 2 hours. For competition assays, an unlabeled oligonucleotide probe was added to the prebinding reaction at 100-fold molar excess over the amount of biotin-labeled probes. Protein-DNA complexes were resolved by nondenaturing polyacrylamide (6%) gel electrophoresis, buffered by 0.25× Tris-borate/EDTA (TBE). The complexes consisting of biotin-labeled DNA and nuclear proteins were electrophoretically transferred to nylon membrane (Hybond-N+; GE Healthcare Life Sciences) and the membrane was irradiated for 5–30 minutes with a 245 nM illuminator and detected by chemiluminescence (Lightshift Chemiluminescent EMSA Kit; Thermo Fisher Scientific).