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