Chromatin Immunoprecipitation (ChIP) Assay

The chromatin immunoprecipitation assay was performed using a Zymo-Spin ChIP kit (Zymo Research, Irvine, CA, USA, Cat. No. D5210) as previous described^{10 (link)}. Chromatin was crosslinked with 1% formaldehyde for 10 min at room temperature. The crosslinking reaction was stopped at a final concentration of 0.125 M glycine. The prepared nuclei were mechanically sheared using the Bioruptor Pico sonication system (Diagenode, Liege, Belgium) at 4 °C in 30 s on/off for 25 cycles. A small portion of the chromatin solution was reserved as input DNA. The chromatin samples were incubated with the indicated antibodies by rotating for 16 h at 4 °C. SureBeads Protein A/G magnetic beads (Bio-Rad, Cat. No. 161-4013) were incubated at 4 °C for 1 h by rotation to elute the antibody-chromatin complexes. The bead-antibody-chromatin complex was washed three times with chromatin wash buffer (Zymo Research, Cat. No. D5210). The eluted chromatin was decrosslinked with 5 M NaCl, and then, the chromatin proteins were degraded with proteinase K (genDEPOT, Katy, TX, USA, Cat. No. P2170). ChIP DNA was purified using a QIAquick Spin column (Qiagen, Hilden, Germany, Cat. No. 28115). The ChIP DNA and input were analyzed via qPCR using primer pairs specific to the target gene promoters. The primer sequences are listed in Supplementary Table 2.