Type III CRISPR-Cas System for Robust RNA Knockdown and Imaging in Eukaryotes

Tech ID: 32820 / UC Case 2022-128-0

Patent Status

Country Type Number Dated Case
United States Of America Published Application 20240026323 01/25/2024 2022-128

Additional Patent Pending

Brief Description

Type III CRISPR-Cas systems recognize and degrade RNA molecules using an RNA-guided mechanism that occurs widely in microbes for adaptive immunity against viruses. The inventors have demonstrated that this multi-protein system can be leveraged for programmable RNA knockdown of both nuclear and cytoplasmic transcripts in mammalian cells.

Using single-vector delivery of the S. thermophilus Csm complex, RNA knockdown was achieved with high efficiency (90-99%) and minimal off-targets, outperforming existing technologies of shRNA- and Cas13-mediated knockdown. Furthermore, unlike Cas13, Csm is devoid of trans-cleavage activity and thus does not induce non-specific transcriptome-wide degradation and cytotoxicity. Catalytically inactivated Csm can also be used for programmable RNA-binding, which the inventors exploit for live-cell RNA imaging. This work demonstrates the feasibility and efficacy of multi-subunit CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes.

Suggested uses

This invention has the potential to completely supplant RNAi and Cas13-based RNA knockdown technologies.

Suggested uses include:

  • research purposes requiring gene perturbation at the transcript (RNA) but not genome (DNA) level.
  • efficiently knocking down both cytoplasmic and nuclear RNAs.
  • RNA imaging in live cells.
  • RNA detection for diagnostic purposes.
  • utilizing the enzyme's ssDNase and/or cyclic oligoadenylate synthesis activities.


The advantages include:

  • yields robust, highly efficient RNA knockdown with minimal off-targets and no cell toxicity
  • cheap, easy to use, and easy to deliver as an all-in-one vector
  • allows for gene perturbation at the transcript (RNA) level
  • efficiently knocks down both cytoplasmic and nuclear RNAs

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  • Doudna, Jennifer A.

Other Information


siRNA, shRNA, knockdown, ncRNA, RNA, Type III, CRISPR, Cas, Csm, Cas13, RNAi

Categorized As

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