Aberrant genome organization is closely correlated to cancer. However, the mechanism by which key cancer factors regulate higher-ordered genome structures for cancer remains to be illustrated. Here, we identify active chromatin loop hubs in colorectal cancer (CRC) cells by β-catenin and H3K4me3 HiChIP. Induction of DNA methylation by dCas9-KRAB-MeCP2 at loop hub area inhibits CRC cell growth. Moreover, β-catenin can form phase-separated condensates both in vitro and in CRC cells, which is associated with β-catenin-mediated loop hubs. dCas9-APEX2 based proximity labeling tools are employed to identify the components of β-catenin condensates at the selected loop hubs. The representative component candidates are further validated by nuclear co-localization via in vitro or in vivo imaging and genome co-binding via ChIP-seq. Within the candidates, FUS seems to be the scaffold protein which facilitates the phase separation ability of β-catenin, while PARP1 and DHX9 are functioned as client proteins which maintain the active environment within loop hub area through H3K4me3. Consequently, loss of the key components, either FUS or PARP1, can suppress CRC growth. Altogether, we provide new insight how cancer factors control genome architectures for cancer growth through phase separation.

β-catenin,Phase Separation,Loop Hubs