DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells
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.
Authors
- Lingyi Chen (ORCID: https://orcid.org/0000-0002-3695-3407)
- Vikas Malik (ORCID: https://orcid.org/0000-0002-9300-6414)
- Francesco Faiola (ORCID: https://orcid.org/0000-0002-3512-8253)
- Effie Apostolou (ORCID: https://orcid.org/0000-0002-8111-0863)
- Mingjiang Xu (ORCID: https://orcid.org/0000-0002-7063-6253)
- Xin Huang (ORCID: https://orcid.org/0000-0001-6778-8849)
- Syed Raza Mahmood (ORCID: https://orcid.org/0000-0003-3418-1383)
- Jihong Yang (ORCID: https://orcid.org/0000-0002-2753-0939)
- Xianle Shi
- Miha Modic (ORCID: https://orcid.org/0000-0002-2894-7218)
- Junjun Ding (ORCID: https://orcid.org/0000-0002-9936-882X)
- Wei Xie (ORCID: https://orcid.org/0000-0003-2126-3849)
- Xichen Bao (ORCID: https://orcid.org/0000-0003-0389-4233)
- Weiyu Zhang (ORCID: https://orcid.org/0000-0002-3383-236X)
- Jianlong Wang (ORCID: https://orcid.org/0000-0002-1317-6457)
- Feng‐Chun Yang (ORCID: https://orcid.org/0000-0001-8524-4095)
- Yanjing Li (ORCID: https://orcid.org/0000-0002-0747-6947)
- Hongwei Zhou (ORCID: https://orcid.org/0000-0003-2472-8541)
- Xiukun Hou
- Yong Chen (ORCID: https://orcid.org/0000-0001-5857-6086)
Institutions
- The University of Texas at San Antonio Health Science Center (US)
- Chinese Academy of Sciences (CN)
- Nankai University (CN)
- Cornell University (US)
- Columbia University Irving Medical Center (US)
- The Francis Crick Institute (GB)
- Guangzhou Institutes of Biomedicine and Health (CN)
- Tianjin Medical University Cancer Institute and Hospital (CN)
- Shanghai Cancer Institute (CN)
- Center for Excellence in Molecular Cell Science (CN)
- University College London (GB)
- Icahn School of Medicine at Mount Sinai (US)
- Tsinghua University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-12-30
- DOI
- https://doi.org/10.1038/s41467-024-55054-8
- Citations
- 7
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 1.64
Funders
- National Natural Science Foundation of China
- National Institutes of Health
- National Institute of General Medical Sciences
- Eunice Kennedy Shriver National Institute of Child Health and Human Development