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Background <p>Aberrant three-dimensional genome organization is a hallmark of cancer. However, the underlying regulatory mechanisms remain elusive.</p> Results <p>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.</p> Conclusions <p>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.</p>

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Phase separation of β-catenin assembles active loop hubs in colorectal cancer

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月19日

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  • Jiyuan Yang,
  • Jun Sun,
  • Hanyi Zhang,
  • Yangyinhui Yu,
  • Feng Chen,
  • Jingyun Mo,
  • Susu Luo,
  • Yang Xu,
  • Linfeng Zhong,
  • Delin Tan,
  • Yingnan Lin,
  • Yujia Liao,
  • Yujia Zhang,
  • Jiaxiu Zhang,
  • Wanting Chen,
  • Xiaona Huang,
  • Yan Peng,
  • Huabin Gao,
  • Huaiming Wang,
  • Qing Gong,
  • Jia Wang

摘要

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.