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Decoding the genomic landscape of chromatin-associated biomolecular condensates

Author

Listed:
  • Zhaowei Yu

    (Tongji University)

  • Qi Wang

    (Tongji University)

  • Qichen Zhang

    (Naval Medical University
    Lingang Laboratory)

  • Yawen Tian

    (Lingang Laboratory)

  • Guo Yan

    (Lingang Laboratory)

  • Jidong Zhu

    (Etern Biopharma)

  • Guangya Zhu

    (Lingang Laboratory)

  • Yong Zhang

    (Tongji University)

Abstract

Biomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identification in vivo. To address this, we develop CondSigDetector, a computational framework designed to detect condensate-like chromatin-associated protein co-occupancy signatures (CondSigs), to predict genomic loci and component proteins of distinct chromatin-associated biomolecular condensates. Applying this framework to mouse embryonic stem cells (mESC) and human K562 cells enable us to depict the high-resolution genomic landscape of chromatin-associated biomolecular condensates, and uncover both known and potentially unknown biomolecular condensates. Multi-omics analysis and experimental validation further verify the condensation properties of CondSigs. Additionally, our investigation sheds light on the impact of chromatin-associated biomolecular condensates on chromatin activities. Collectively, CondSigDetector provides an approach to decode the genomic landscape of chromatin-associated condensates, facilitating a deeper understanding of their biological functions and underlying mechanisms in cells.

Suggested Citation

  • Zhaowei Yu & Qi Wang & Qichen Zhang & Yawen Tian & Guo Yan & Jidong Zhu & Guangya Zhu & Yong Zhang, 2024. "Decoding the genomic landscape of chromatin-associated biomolecular condensates," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51426-2
    DOI: 10.1038/s41467-024-51426-2
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