Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells [CTCF-HA-ChIP]

CTCF is the most studied transcription factor, which is essential for chromatin interaction maintenance. Although several independent studies reported that CTCF protein could pull down RNAs in vitro and in cells, there are continuous debates about authenticity of the RNA-binding affinity of CTCF and its biological role, mainly due to the concerns of limited research techniques such as CLIP-seq. To systematically investigate the RNA-interaction with CTCF and the impact on gene regulation, we conducted in vivo CTCF ChIP-seq under three conditions, including RNase A treatment, Triptolide-mediated transcription inhibition and auxin-inducible degron mediated RNA-binding domain mutant swap. Our results consistently suggest that when RNA-interaction with CTCF protein was impaired in vivo, the DNA occupancy of CTCF remains the same at the genome-wide scale. Our data provide a complementary approach and in silico evidence to re-considerate the role of RNA-binding affinity of CTCF.