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Controlling and enhancing CRISPR systems


Many bacterial and archaeal organisms use clustered regularly interspaced short palindromic repeats–CRISPR associated (CRISPR–Cas) systems to defend themselves from mobile genetic elements. These CRISPR–Cas systems are classified into six types based on their composition and mechanism. CRISPR–Cas enzymes are widely used for genome editing and offer immense therapeutic opportunity to treat genetic diseases. To realize their full potential, it is important to control the timing, duration, efficiency and specificity of CRISPR–Cas enzyme activities. In this Review we discuss the mechanisms of natural CRISPR–Cas regulatory biomolecules and engineering strategies that enhance or inhibit CRISPR–Cas immunity by altering enzyme function. We also discuss the potential applications of these CRISPR regulators and highlight unanswered questions about their evolution and purpose in nature.

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Fig. 1: Transcriptional modulation of a CRISPR locus under diverse environments.
Fig. 2: Summary of the different strategies utilized by Acrs to inhibit CRISPR activity.
Fig. 3: cOA signaling in type III CRISPR systems.
Fig. 4: Fine tuning type III CRISPR–Cas immunity.
Fig. 5: Potential mechanisms of CRISPR-associated accessory proteins.
Fig. 6: Engineered regulation of CRISPR–Cas biogenesis and interference.


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We thank T.Y. Liu for helpful discussions and proofreading the manuscript. This research was developed with funding from the Defense Advanced Research Projects Agency (DARPA) award HR0011-17-2-0043. The views, opinions, and/or findings expressed are those of the author and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. This material is based upon work supported by the National Science Foundation under award number 1817593. Research reported in this publication was supported by the National Institutes of Health under award number grant award U19AI135990 (Host Pathogen Map Initiative). This research was supported by the Allen Distinguished Investigator Program, through The Paul G. Allen Frontiers Group. B.F.C. is supported by an NIH/NIGMS postdoctoral fellowship (F32 GM131654). G.J.K. is supported by an NHMRC Investigator Grant (ELI, 1175568).

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Correspondence to Jennifer A. Doudna.

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The Regents of the University of California have patents issued and pending for CRISPR technologies on which H.S., B.F.C., G.J.K. and J.A.D. are inventors. J.A.D. is a cofounder of Caribou Biosciences, Editas Medicine, Scribe Therapeutics, Intellia Therapeutics and Mammoth Biosciences. J.A.D. is a scientific advisory board member of Caribou Biosciences, Intellia Therapeutics, eFFECTOR Therapeutics, Scribe Therapeutics, Mammoth Biosciences, Synthego, Algen Biotechnologies, Felix Biosciences and Inari. J.A.D. is a Director at Johnson & Johnson and has research projects sponsored by Biogen, Pfizer, AppleTree Partners and Roche.

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Shivram, H., Cress, B.F., Knott, G.J. et al. Controlling and enhancing CRISPR systems. Nat Chem Biol 17, 10–19 (2021).

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