CTCF-mediated chromatin looping is coupled to the formation of phase-separated transcriptional condensate.

Abstract

The CCCTC-binding factor (CTCF) is thought as one of essential architectural proteins along with cohesin for chromatin loop formation in the mammalian genome structure. Recent live-cell imaging approaches have observed some key transcription factors form condensates in a manner of transcription dependence, while the spatial base of the transcriptional condensates in the genome structure has not been addressed. Here, we investigated whether the formation of transcriptional condensates is related to chromatin loop formation by CTCF. We used the auxin-inducible degron (AID) system for acute conditional depletion and restoration of CTCF. With RNA Polymerase II (Pol II) Hi-Chip, we found chromatin loops are dramatically reduced upon CTCF depletion, especially on super-enhancers. In addition, our super-resolution fluorescence imaging found that transcriptional condensates are mostly dissolved upon CTCF depletion, which come back upon CTCF restoration. Taken together, our results indicate that chromatin loop formation by CTCF is crucial to the formation of transcriptional condensates in the cell nucleus, as a spatial groundwork in the genome structure.