CUT&Tag sequencing analyses target genes directly bound by transcription factors

TF occupancy within or near a gene promoter or enhancer region is often assumed to be sufficient evidence for the gene to be classified as a direct TF target. We identified the TF ATF3 and ONECUT2 occupancy sites and direct target candidate genes using the CUT&Tag in hepatocyte organoids. We isolated hepatocytes from C57BL/6 adult male mice for organoids culture, and genomic DNA of hepatocyte organoids was extracted and applied to CUT&Tag.