Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping

In human cells, CTCF's role in genomic organization and global transcription regulation is less clearly defined due to the lack of available tools to efficiently deplete CTCF. Here, we used an auxin-inducible degron system to conditionally deplete CTCF in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM. Cut & Run ChIP-seq showed acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ~1.8 Mb downstream. Overall design: CUT&RUN ChIP-seq was performed on auxin-inducible degron system to conditionally deplete CTCF in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM, using antibodies against CTCF for a pulldown assay