ChIP Profiling of NTL8 Protein

NTL8 protein ChIP experiments were carried out following the methods described in Zhao et al. (2020) (link). Briefly, nuclei were extracted from 3 g of materials with 30 mL of Honda buffer (0.4 M sucrose, 2.5% Ficoll, 5% dextran T40, 25 mM Tris-HCl at pH 7.4, 10 mM MgCl₂, 0.5% Triton X-100, 0.5 mM PMSF, proteinase inhibitor cocktail [Roche 04693159001], 5 mM DTT). After nuclei extraction, purified nuclei were lysed by RIPA buffer (1× PBS, 1% Igepal CA-630 [Sigma I8896], 0.5% sodium deoxycholate, 0.1% SDS, proteinase inhibitor cocktail) and then fragmented by sonication (Diagenode Bioruptor). After sonication, the fragmented chromatin extract was cleared by centrifugation at 13,000 rpm for 15 min at 4°C before immunoprecipitation. The immunoprecipitations were performed with GFP-trap beads (Chromotek GTMA-20) for GFP-NTL8-D2 (Fig. 2G) and anti-HA magnetic beads (Pierce 88836) for HA-NTL8 (Supplemental Fig. S4H) in the ntl8-OE3 line. Relevant primers are listed in Supplemental Table S3.