The ChIP and input DNA libraries were prepared as previously described (34, 57). Briefly, 10 million HepG2 cells were cross-linked with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine. The chromatin was fragmented and then immunoprecipitated with Protein A + G magnetic beads coupled with antibodies against SMRC1, SATB1, and NFIC. After reverse cross-linking, ChIP and input DNA fragments were used for library construction with NEBNext Ultra Ligation Module (NEB, no. E7445). The DNA libraries were amplified and subjected to deep sequencing with an Illumina sequencer. The ChIP-seq data processing was performed as we reported recently (57). Cis-regulatory sequence elements that mediate the binding of SMRC1, SATB1, or NFIC were predicted with MEME-ChIP (58).

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