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Modulating gene regulation function by chemically controlled transcription factor clustering

Author

Listed:
  • Jiegen Wu

    (Peking University
    Peking University
    Peking University
    Tsinghua University)

  • Baoqiang Chen

    (Tsinghua University)

  • Yadi Liu

    (Peking University
    Peking University
    Peking University)

  • Liang Ma

    (Peking University
    Peking University
    Peking University)

  • Wen Huang

    (Peking University
    Peking University
    Peking University)

  • Yihan Lin

    (Peking University
    Peking University
    Peking University)

Abstract

Recent studies have suggested that transcriptional protein condensates (or clusters) may play key roles in gene regulation and cell fate determination. However, it remains largely unclear how the gene regulation function is quantitatively tuned by transcription factor (TF) clustering and whether TF clustering may confer emergent behaviors as in cell fate control systems. Here, to address this, we construct synthetic TFs whose clustering behavior can be chemically controlled. Through single-parameter tuning of the system (i.e., TF clustering propensity), we provide lines of evidence supporting the direct transcriptional activation and amplification of target genes by TF clustering. Single-gene imaging suggests that such amplification results from the modulation of transcriptional dynamics. Importantly, TF clustering propensity modulates the gene regulation function by significantly tuning the effective TF binding affinity and to a lesser extent the ultrasensitivity, contributing to bimodality and sustained response behavior that are reminiscent of canonical cell fate control systems. Collectively, these results demonstrate that TF clustering can modulate the gene regulation function to enable emergent behaviors, and highlight the potential applications of chemically controlled protein clustering.

Suggested Citation

  • Jiegen Wu & Baoqiang Chen & Yadi Liu & Liang Ma & Wen Huang & Yihan Lin, 2022. "Modulating gene regulation function by chemically controlled transcription factor clustering," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30397-2
    DOI: 10.1038/s41467-022-30397-2
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    References listed on IDEAS

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    Cited by:

    1. Rui Chen & Xinyao Shi & Xiangrui Yao & Tong Gao & Guangyu Huang & Duo Ning & Zemin Cao & Youxin Xu & Weizheng Liang & Simon Zhongyuan Tian & Qionghua Zhu & Liang Fang & Meizhen Zheng & Yuhui Hu & Huan, 2024. "Specific multivalent molecules boost CRISPR-mediated transcriptional activation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Ying Liang & Haiyue Xu & Tao Cheng & Yujuan Fu & Hanwei Huang & Wenchang Qian & Junyan Wang & Yuenan Zhou & Pengxu Qian & Yafei Yin & Pengfei Xu & Wei Zou & Baohui Chen, 2022. "Gene activation guided by nascent RNA-bound transcription factors," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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