Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping

Flores, J. P.; Perreault, A.; Drum, Z. A.; Xu, C.; Cruz Alonso, D.; Petros, G.; Wu, Y.; Kim, H.; Quiroga-Barber, I. Y.; Sahasrabudhe, I.; Demmerle, J.; Wang, G. G.; Cai, D.; Phanstiel, D. H.

doi:10.64898/2025.12.19.695003

bioRxiv · 10.64898/2025.12.19.695003

Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping

Flores, J. P.·Perreault, A.·Drum, Z. A.·Xu, C.·Cruz Alonso, D.·Petros, G.·Wu, Y.·Kim, H.·Quiroga-Barber, I. Y.·Sahasrabudhe, I.·Demmerle, J.·Wang, G. G.·Cai, D.·Phanstiel, D. H.

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Abstract

Cells continually face environmental stressors that challenge homeostasis, yet how three-dimensional (3D) chromatin structure contributes to these stress responses remains unclear under hyperosmotic conditions. To investigate this, we map 3D chromatin structure, its molecular drivers, and transcriptional outcomes during sorbitol-induced hyperosmotic stress. Within 1 hour of sorbitol treatment, pre-existing loops and domains collapse, while several hundred de novo sorbitol-induced loops emerge. These loops are punctate, longer-range, and transient. 3D chromatin structure largely returns to baseline conditions by 24 hours. Loop reorganization is consistent across cell types and hyperosmotic stimuli. Sorbitol-induced loops require cohesin but not CTCF, and anchors are enriched at active promoters harboring GC-rich transcription factor motifs. Genes at these anchors show delayed activation following loop formation, consistent with loops acting upstream of transcription. Together, hyperosmotic stress triggers rapid, reversible, CTCF-independent chromatin reorganization that correlates with transcriptional adaptation.

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Flores, J. P., Perreault, A., Drum, Z. A., Xu, C., Cruz Alonso, D., Petros, G., Wu, Y., Kim, H., Quiroga-Barber, I. Y., Sahasrabudhe, I., Demmerle, J., Wang, G. G., Cai, D., Phanstiel, D. H.. 2025-12-22. Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping. https://doi.org/10.64898/2025.12.19.695003

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