Magnetic chip kit

The ChIP assays were performed using the Magnetic ChIP kit (Millipore) according to the manufacturer’s instructions. Briefly, H1650 and PC-9 cells were fixed by 1% formaldehyde, fragmented by a combination of MNase and sonication. SETD2 (Active Motif) and H3K36me3 (Active Motif) antibodies were then used for immunoprecipitation. After washing and reverse-crosslinking, the precipitated DNA was amplified by CXCL1 promoter primers and then quantified by the Step-One Plus Real-Time PCR System and DNA gel electrophoresis.

Total RNA was subjected to MGI2000 performed by BGI Tech Solutions Co., Ltd. Transcriptomic reads were mapped to reference genome (mm10) using Bowtie software, and gene expression levels were quantified using the RSEM software package. The list of significantly affected genes was obtained by setting a false discovery rate (FDR) threshold of 0.001, P-value < 0.0,1 and fold changes greater than 1.2 or log2Fc < −0.75. Manual curation of GOs was performed using KEGG or Enrichr and visualized in the form of a heatmap using −Log10(P-value). Gene expression datasets were deposited into the GEO database (GSE159351 and GSE159352). The ChIP assays were performed using the Magnetic ChIP kit (Millipore). The procedure was as described in the kit provided by the manufacturer. Briefly, isolated HCT116 cells were fixed by 1% formaldehyde, fragmented by sonication. EZH2 (Cell Signaling Technology, 5246 S) and H3K27Ac (Cell Signaling Technology, 8173 S) were then used for immunoprecipitation. After washing and reverse-crosslinking, the precipitated DNA was amplified by primers and quantified by the qPCR. Primer sequences can be found in Supplementary Table 4.