Abstract

Background Aberrant three-dimensional genome organization is a hallmark of cancer. However, the underlying regulatory mechanisms remain elusive. Results Here, we identify β-catenin associated loop hubs in colorectal cancer HCT116 cells using HiChIP profiling. These hubs exhibit an active transcriptional environment marked by elevated gene expression and H3K4me3 enrichment. Disruption of loop hub formation by artificial DNA methylation suppresses hub gene expression and inhibits colorectal cancer growth, indicating its functional importance in cancer. Mechanistically, β-catenin forms phase-separated condensates that are closely associated with loop hubs. By proximity labeling and genomic analyses, we identify and validate the components within β-catenin condensates at loop hubs. We further characterize FUS as a structural scaffold for β-catenin condensate assembly, whereas PARP1 maintains active transcription via H3K4me3. Depletion of either component attenuates condensate function through distinct regulatory mechanisms. Conclusions Our findings reveal that β-catenin condensates orchestrate gene regulatory networks by assembling higher-order chromatin architecture, providing new insights into a mechanistic link between phase separation, genome organization and cancer progression.