Chromatin is spatially organized into three-dimensional structures at different levels including A/B compartments, topologically associating domains and loops. The canonical CTCF-mediated loop extrusion model can explain the formation of loops. However, the organization mechanisms underlying long-range chromatin interactions such as interactions between A–A compartments are still poorly understood. Here we show that different from the canonical loop extrusion model, RYBP-mediated phase separation of CTCF organizes inter-A compartment interactions. Based on this model, we designed and verified an induced CTCF phase separation system in embryonic stem cells (ESCs), which facilitated inter-A compartment interactions, improved self-renewal of ESCs and inhibited their differentiation toward neural progenitor cells. These findings support a novel and non-canonical role of CTCF in organizing long-range chromatin interactions via phase separation.

染色质在空间上组织成不同级别的三维结构，包括 A/B 区室、拓扑关联域和环。经典的 CTCF 介导的环挤出模型可以解释环的形成。然而，人们对长程染色质相互作用（例如 A-A 区室之间的相互作用）的组织机制仍然知之甚少。在这里，我们表明，与典型的环挤出模型不同，RYBP 介导的 CTCF 相分离组织了 A 室间相互作用。基于该模型，我们在胚胎干细胞（ESC）中设计并验证了诱导CTCF相分离系统，该系统促进A室间相互作用，改善ESC的自我更新并抑制其向神经祖细胞的分化。这些发现支持 CTCF 在通过相分离组织长程染色质相互作用方面具有新颖且非规范的作用。