ChIP-qPCR Assay for Protein-DNA Interactions

ChIP was performed according to the manual of the SimpleChIP® Enzymatic Chromatin IP Kit (#9003, Cell Signaling Technology) [34 (link)]. Crosslinking of protein-DNA complexes was achieved with 1% formaldehyde before lysis (See Western blot methods). The lysed samples were sonicated to shear the chromatin and then incubated overnight with antibodies (Anti-p53: Cat. # 17-613, Millipore; Anti-acetyl-Histone H4: Cat. # 06-866, Millipore; Anti-acetyl-Histone H3: Cat. # 06-599, Millipore; Anti-Dnmt3a: ab2850, Abcam; Anti-Dnmt1: ab13537, Abcam; Anti-Dnmt3b: ab122932, Abcam) or normal IgG (#2729, Cell Signaling Technology) at 4 °C, followed by capture with protein A/G magnetic beads (#9006, Cell Signaling Technology) for 2 h. Then DNA was purified for the subsequent qPCR assays. ChIP-qPCR primers are listed in table S1.