Cells were cross-linked with 1% formaldehyde for 10 min at room temperature. The reaction was quenched by 0.125 M glycine for 5 min. Fixed cells were lysated with ChIP lysis buffer 1 [50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 1% Triton X-100, and 0.1% deoxycholate] on ice and lysis buffer 2 [10 mM tris (pH 8.0), 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA] at room temperature. Chromatin was digested with MNase (Cell Signaling Technology) in digestion buffer [10 mM tris (pH 8.0), 1 mM CaCl2, and 0.2% Triton X-100] at 37°C for 15 min. The nucleus was broken down by one pulse of bioruptor with high output. The following antibodies were used for ChIP or ChIP-seq: rabbit anti-ARID1A (Abcam, catalog no. ab182560), rabbit anti-NCAPH2 (Bethyl, catalog no. A302-276A), rabbit anti-H3K4me1 (Abcam, catalog no. ab8895), rabbit anti-H3K4me3 (Active Motif, catalog no. 39159), rabbit anti-H3K9me2 (Cell Signaling Technology, catalog no. 4568), rabbit anti-H3K27ac (Abcam, catalog no. ab4729), rabbit anti–Pol II (Santa Cruz, catalog no. sc-47701), and rabbit anti-SNF5 (Bethyl, catalog no. A301-087A). Chromatin was incubated overnight at 4°C, and Protein A/G Dynabeads were added to the reaction for another 1.5 hours. Magnetic beads were washed, and chromatin was eluted. Eluted DNA was treated with proteinase K at 55°C for 45 min and decross-linked at 65°C overnight. A Zymo ChIP DNA clean and concentrator kit (Zymo Research, catalog no. D5205) was used to purify the ChIP DNA. ChIP DNA was used for ChIP-qPCR or ChIP-seq.

For ChIP-qPCR, the following primers were used: CDH6 locus, 5′-TCCCATGAAAGTCTCAGGAATG-3′ (forward) and 5′-AGACACTGGGTTTCCTCTCTA-3′ (reverse); KCNK5 locus, 5′-AGGGCCTGAGTTAGCATTTC-3′ (forward) and 5′-TCAGGGTCTTAGGTCTCAGATT-3′ (reverse); PROM1 locus, 5′-GCATCCACTTGGCATGATATTG-3′ (forward) and 5′-GAAGCTGGTCTCATACAGGATTTA-3′ (reverse); AGPAT4 locus, 5′-CCCAAAGTCACTCCAGTGATAG-3′ (forward) and 5′-GAACGGGTCTCTGTTGCTATT-3′ (reverse); LAMA4 locus, 5′-CACTGTGAGTACCATCCCTTT-3′ (forward) and 5′-GAGTTTCAGTCCCATCCTTCTT-3′ (reverse); and HGD locus, 5′-CATCCAGATCCAAGACCAAGAC-3′ (forward) and 5′-CCTGGTGTCTTGTGGCTAAA-3′.

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