DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells
Xianle Shi, Yanjing Li, Hongwei Zhou, Xiukun Hou, Jihong Yang, Vikas Malik, Francesco Faiola, Junjun Ding, Xichen Bao, Miha Modic, Weiyu Zhang, Lingyi Chen, Syed Raza Mahmood, Effie Apostolou, Feng‐Chun Yang, Mingjiang Xu, Wei Xie, Xin Huang, Yong Chen, Jianlong Wang
Abstract
Pluripotent stem cells possess a unique nuclear architecture characterized by a larger nucleus and more open chromatin, which underpins their ability to self-renew and differentiate. Here, we show that the nucleolus-specific RNA helicase DDX18 is essential for maintaining the pluripotency of human embryonic stem cells. Using techniques such as Hi-C, DNA/RNA-FISH, and biomolecular condensate analysis, we demonstrate that DDX18 regulates nucleolus phase separation and nuclear organization by interacting with NPM1 in the granular nucleolar component, driven by specific nucleolar RNAs. Loss of DDX18 disrupts nucleolar substructures, impairing centromere clustering and perinucleolar heterochromatin (PNH) formation. To probe this further, we develop NoCasDrop, a tool enabling precise nucleolar targeting and controlled liquid condensation, which restores centromere clustering and PNH integrity while modulating developmental gene expression. This study reveals how nucleolar phase separation dynamics govern chromatin organization and cell fate, offering fresh insights into the molecular regulation of stem cell pluripotency. Pluripotent stem cells depend on specialized nuclear organization for their function. Here, the authors show that DDX18 regulates nucleolar phase separation and chromatin architecture to preserve human embryonic stem cell pluripotency.