Advanced auxin-inducible degron system deciphers unique functions of CTCF in transcriptional regulation [ChIP-seq]

ChIPseq was performed on cells depleted for CTCF by AID2 auxin degradation to examine CTCF DNA binding affinity. ChIP seq was also performed on cells depleted for endogenous CTCF and expressing HA tagged WT CTCF and CTCF mutants (deltaZF1, deltaZF10 and deltaRBR) to examine how functional deletions affect CTCF DNA binding affinity. Overall design: AID2 auxin degradation was combined with endogenous AID tagged CTCF in the human B-ALL cell line SEM. Cells were depleted for endogenous CTCF and induced to express HA tagged WT CTCF and CTCF mutants (deltaZF1, deltaZF10 and deltaRBR). ChIPseq was performed to examine CTCF DNA binding affinity.