Chromatin immunoprecipitation was performed using a previously described protocol (53 (link)). Briefly, 1 million cells were fixed with 1% formaldehyde and sonicated with Covaris E220 or Bioruptor Plus. Sonicated chromatin was then incubated with antibodies against target proteins or histone posttranslational modifications overnight. Protein A/G beads (Thermo Fisher) were added to the sonicated chromatin for 2 hours. After washes with low-salt, high-salt, and LiCl wash buffer, beads were decross-linked with proteinase K (Zymo Research) at 55°C overnight. Pulled-down DNA was extracted by the DNA clean and concentration kit (Zymo Research). Libraries were prepared using the Swift Bioscience Acce-NGS 2G plus kit according to the manufacturer's manual. The libraries were sequenced 150-bp paired-end on HiSeq 2000 by Fulgent Genomics.
Chromatin immunoprecipitation sequencing (ChIP-seq) antibodies used in this study included H3K27ac (Diagenode, Rabbit Polyclonal, C15410196, RRID:AB_2637079), H3K27me3 (Cell Signaling Technology, Rabbit Monoclonal, 9733, RRID:AB_2616029), Pol II S5P (Diagenode, Mouse Monoclonal, C15200007, RRID:AB_2713926), HDAC1 (Diagenode, Rabbit Polyclonal, C15410325, RRID:AB_2921266), anti-FLAG antibody (Sigma-Aldrich, mouse monoclonal, F1804, RRID:AB_262044), and anti-HA antibody (Abcam, Rabbit Polyclonal, ab9110, RRID:AB_307019).