HP1ß dependent phase separation regulates embryonic stem cells exit from naïve pluripotent state

Liquid-liquid phase separation has drawn great attention as a physical process that mediates the formation of membraneless organelles in cells to coordinate biological reactions in space and time. Previously, it was proposed that the formation of phase-separated droplets is a unique property of HP1a. Here, we show that HP1ß, but not HP1a and HP1?, forms nucleosome dependent phase separated droplets. We demonstrate that H3K9me3 is required for HP1ß dependent phase separation. Importantly, HP1ß dependent phase separation regulates heterochromatin formation, thus controlling embryonic stem cells differentiation. In response to pluripotency exit, HP1ß is phosphorylated at serine 89 recruiting KAP1, a pluripotency regulator, and sequestering it in the heterochromatin compartment. This induces changes in the level of pluripotency factors and triggers pluripotency exit. We propose that such a trapping mechanism creates a fast and dynamic mode of remote control of gene expression to regulate cell fate decisions solely based on membraneless organelles.