biostudies-literatureLiu NQEuropean Research CouncilDutch Ministry of Health, Welfare and SportDutch Research Council (NWO)Dutch Cancer Societygkaf549https://www.ebi.ac.uk/biostudies/studies/S-EPMC12207409biostudies-literatureUnknown53(12)Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effect relationships remain largely unknown. In this study, we use acute degradation of WAPL, CTCF and cohesin in mouse embryonic stem cells to investigate the dynamics of loop extrusion and its relationship to compartmentalisation. Stabilisation of cohesin on chromatin by depletion of WAPL results in the formation of extended loops and promotes looping between non-convergent CTCF sites. Loss of WAPL also results in a rapid decrease in compartmentalisation, which is reversed by subsequent removal of cohesin, directly demonstrating the opposite role of extrusion on compartmentalisation. Using combined depletion of WAPL and CTCF, we identify fountains, aNucleic acids researchExtrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers.PMC12207409865459637587VI.C.222.049016.Veni.181.014016.161.316Schijns MMGAMagnitov MLiu NQde Wit ETeunissen Hvan Schaik Tvan Steensel BfalseExtrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers.Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effect relationships remain largely unknown. In this study, we use acute degradation of WAPL, CTCF and cohesin in mouse embryonic stem cells to investigate the dynamics of loop extrusion and its relationship to compartmentalisation. Stabilisation of cohesin on chromatin by depletion of WAPL results in the formation of extended loops and promotes looping between non-convergent CTCF sites. Loss of WAPL also results in a rapid decrease in compartmentalisation, which is reversed by subsequent removal of cohesin, directly demonstrating the opposite role of extrusion on compartmentalisation. Using combined depletion of WAPL and CTCF, we identify fountains, a2025-01-01T00:00:00Z2025 Jun2026-04-08T15:41:19.812Z2026-04-08T05:18:42.774ZS-EPMC122074094058630910.1093/nar/gkaf549