Specific multivalent molecules boost CRISPR-mediated transcriptional activation

  • Nat Commun. 2024 Aug 22;15(1):7222. doi: 10.1038/s41467-024-51694-y.
Rui Chen  1  2  3  4 ,  Xinyao Shi  1  3 ,  Xiangrui Yao  1  3 ,  Tong Gao  1  3 ,  Guangyu Huang  1  3 ,  Duo Ning  1  3 ,  Zemin Cao  1  3 ,  Youxin Xu  1  3 ,  Weizheng Liang  1  3  5 ,  Simon Zhongyuan Tian  1  2  3 ,  Qionghua Zhu  1  2  3  4 ,  Liang Fang  1  2  3  4 ,  Meizhen Zheng  1  2  3 ,  Yuhui Hu  6  7 ,  Huanhuan Cui  8  9  10  11 ,  Wei Chen  12  13  14  15
Affiliations
  • 1. Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
  • 2. Innovative Center for RNA Therapeutics (ICRT), School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
  • 3. Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
  • 4. Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China.
  • 5. Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
  • 6. Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
  • 7. Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
  • 8. Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 9. Innovative Center for RNA Therapeutics (ICRT), School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 10. Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 11. Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 12. Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 13. Innovative Center for RNA Therapeutics (ICRT), School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 14. Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [email protected].
  • 15. Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China. [email protected].
PMID: 39174527 DOI: 10.1038/s41467-024-51694-y
Abstract

CRISPR/Cas-based transcriptional activators can be enhanced by intrinsically disordered regions (IDRs). However, the underlying mechanisms are still debatable. Here, we examine 12 well-known IDRs by fusing them to the dCas9-VP64 activator, of which only seven can augment activation, albeit independently of their phase separation capabilities. Moreover, modular domains (MDs), another class of multivalent molecules, though ineffective in enhancing dCas9-VP64 activity on their own, show substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and fusing dCas9-VP64 with different IDRs/MDs, we uncover that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs yields synergistic effects, which can be further amplified via enhancing chromatin interactions. Overall, our study develops a versatile platform for efficient gene activation and sheds important insights into CRIPSR-based transcriptional activators enhanced with multivalent molecules.

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