Capture-C was performed, as previously described (30). Two biotinylated DNA oligonucleotides were designed for both ends of the region containing the rs55958994 SNP, with the following sequence.

(5′ to 3′):



22Rv1 cells (1 × 107) were used to generate a standard 3C library with DpnII digestion. The purified 3C library DNA was then sheared to 200- to 300-bp fragments using sonication. The precapture DNA libraries were prepared using the NEBNext DNA Library Kit according to the manufacturer’s instructions (E6040, E7335, and E7500; New England BioLabs). The biotinylated probes and streptavidin beads (Invitrogen) were used to enrich the bait and its linked chromatin loci by two rounds of hybridization-capture approach. The barcoded Capture-C libraries were sequenced as 150-bp paired-end reads using the Illumina HiSeq 4000 platform. Capture-C data were analyzed on the basis of pipeline proposed by Davies et al. (30).

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