Phase separation of DUX family proteins drives totipotent-like state via 3D genome reorganization and retrotransposon activation

  • Protein Cell. 2026 Mar 14:pwag014. doi: 10.1093/procel/pwag014.
Leilei Gao  1  2  3 ,  Qifeng Gao  1  2  3 ,  Na Hai  4 ,  Ziqiang Wu  5 ,  Penghui Li  5 ,  Han Kang  1  2  3 ,  Xiaohui Song  1  2  3 ,  Jinlian Hua  1  2  3 ,  Shiqiang Zhang  1  2  3 ,  Gang Ren  3  6 ,  Jihong Yang  7 ,  Leqian Yu  8 ,  Yulei Wei  4 ,  Junjun Ding  5 ,  Fan Yang  1  9  2  3
Affiliations
  • 1. College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
  • 2. Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Yangling, 712100, China.
  • 3. Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
  • 4. State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
  • 5. RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
  • 6. Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
  • 7. BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311121, China.
  • 8. Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
  • 9. Northwest A&F University Shenzhen Research Institute, Shenzhen, 518057, China.
PMID: 41832971 DOI: 10.1093/procel/pwag014
Abstract

The acquisition of totipotency requires transcriptional activation of endogenous retroviruses (MERVL/HERVL) and zygotic genome activation (ZGA) related genes, yet the molecular mechanisms linking chromatin architecture to this process remain elusive. Here, we demonstrate that mouse Dux and human DUX4, double homeobox transcription factors essential for totipotency, form liquid-liquid phase-separated (LLPS) condensates through conserved arginine residues within intrinsically disordered regions (IDRs) in the Homeobox domain. These condensates recruit CBP/p300 and CTCF to establish super-enhancers (SEs) at MERVL/MT2 loci, enabling H3K27ac deposition and chromatin accessibility. Hi-C analysis revealed that DUX-driven phase separation facilitates 3D genome reorganization, including de novo formation of enhancer-promoter loops and TAD boundary shifts. Disruption of LLPS (DUXR70A) abolished SE assembly, transcriptional activation, and embryonic chimerism. Strikingly, human DUX4 required phase separation for both myotoxic gene activation and cytotoxicity in facioscapulohumeral muscular dystrophy (FSHD) models. Our study establishes a paradigm wherein phase separation integrates transcriptional control with 3D genome remodeling to license totipotency, with direct implications for developmental biology and disease therapy.

Keywords
3D genome reorganization; DUX; MERVL; phase separation; super-enhancers; totipotency-like state.
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