BMAL1 regulates circadian rhythms via phase separation-mediated transcriptional hub formation

  • Signal Transduct Target Ther. 2026 May 1;11(1):160. doi: 10.1038/s41392-026-02711-7.
Wenzhen Gao  1  2 ,  Li Zhu  1  3 ,  Yali Wei  1  4 ,  Guowen Luo  1  2 ,  Jiahe Wang  1  2 ,  Lijie Wang  1  2 ,  Zhengying Peng  1 ,  Xuan Li  1 ,  Zhuoxuan Wu  1  2 ,  Jingyi Li  1  2 ,  Yanfen Wu  1  2 ,  Xiaoxiao Wang  1  2 ,  Junjun Jing  1 ,  Shujuan Zou  1  3 ,  Qing Zhao  1  3 ,  Yi Fan  5  6 ,  Quan Yuan  7 ,  Chenchen Zhou  8  9
Affiliations
  • 1. State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
  • 2. Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
  • 3. Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
  • 4. Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
  • 5. State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China. [email protected].
  • 6. Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China. [email protected].
  • 7. State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China. [email protected].
  • 8. State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China. [email protected].
  • 9. Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China. [email protected].
PMID: 42062246 DOI: 10.1038/s41392-026-02711-7
Abstract

The mechanisms by which core clock components are spatially organized to ensure robust oscillations in mammals remain unclear. Here, we identify the positive limb factor BMAL1 as a phase-separating protein that forms dynamic biomolecular condensates essential for circadian transcription and behavior. Endogenous BMAL1 forms nuclear puncta that oscillate in sync with the circadian cycle. Deletion analysis and optogenetic clustering identify an N-terminal 90-amino acid intrinsically disordered region whose phosphorylation state tunes BMAL1 phase separation. Besides, BMAL1 condensates behave as multi-molecular assemblies that selectively recruit CLOCK, p300, MED1, and are specifically promoted by E-box DNA. Functionally, an IDR-deleted BMAL1 mutant fails to rescue rhythmic transcription in Bmal1-KO cells and cannot restore locomotor rhythms when reintroduced into SCN-specific Bmal1‑KO mice. These findings establish BMAL1 condensates as dynamic transcriptional hubs that couple phase separation to circadian rhythm in cells and in vivo.

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