CUT&Tag assay showed that SETD1A and H3K4me3 co-occupied the promoters of some known drivers of HCC stemness, such as PRMT6, BMI1, SOX9, ZIC2, ANGPTL4, PDK4, and IRAK1 (24), suggesting SETD1A activated the transcription of these genes. Here, SOX9 is linked to hepatocellular carcinoma.