Streptavidin c 1 bead

H3K27ac HiChIPs from LCLs conditional for EBNA3A expression were performed as previously described^{45 (link)} using H3K27ac antibody (Abcam). Briefly, 1 × 10⁷ cells for each biological replicate were collected and cross-linked by 1% formaldehyde for 10 min. Chromatin was digested using MboI restriction enzyme (New England Biolabs). DNA ends were filled in with Biotin-14-dATP (Thermo Fisher) and other nucleotides and then ligated. After sonication, sheared chromatin was pre-cleared and 3-fold diluted as described in ChIP method and then incubated with 4ug anti-H3K27ac antibody at 4 °C for overnight. Chromatin-antibody complex was captured by Dynabead Protein-A bead, followed by capture with Streptavidin C-1 bead (Thermo Fisher). Libraries were generated using Tn5 followed by PCR. HiChIP samples were size selected by PAGE purification (300–700 bp). All libraries were sequenced on the Illumina NextSeq 500. Each sample has an average depth of ~20 million reads.

HiChIP was performed as previously described^{44 (link)}. Briefly, ~10 million cells were crosslinked in 1% formaldehyde for 10 min at room temperature and then quenched by 125 mM glycine. After washing in PBS, the crosslinked cells were lysed in Hi-C lysis buffer (10 mM NaCl, 10 mM Tris-HCl, 0.2% NP-40, and 1 × protease inhibitor) and digested by MboI restriction enzyme (NEB-R0147). The biotin-dATP (Thermo 19524016) was incorporated to DNA in a fill-in master mix containing DNA polymerase I (NEB-M0210). After ligation and sonication, the sheared chromatin was incubated together with Protein A beads and anti-H3K27ac antibody (Abcam, ab4729, 5 μg per sample) or AR antibody (Santa Cruz sc-816, 5 μg per sample) for overnight at 4 °C with rotation. ChIPed DNA was purified from the eluted chromatin using Zymo DNA Clean & Concentrator kit. Biotin-labeled DNA was captured by Streptavidin C-1 bead (Thermo Fisher, Cat#65002) and fragmented by Tn5 enzyme to generate libraries for high throughput sequencing. Next-generation sequencing was conducted on a HiSeq4000 machine with 150 bp paired-end reads.