Home NATURALEZA Biology and applications of CRISPR–Cas12 and transposon-associated homologs

Biology and applications of CRISPR–Cas12 and transposon-associated homologs

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  • Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van der Oost, J. in CRISPR: Biology and Applications (eds Barrangou, R., Sontheimer, E. J. & Marraffini, L. A.) Ch. 3 (Wiley, 2022).

  • van der Oost, J., Jore, M. M., Westra, E. R., Lundgren, M. & Brouns, S. J. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401–407 (2009).

    Article 
    PubMed 

    Google Scholar
     

  • Mohanraju, P. et al. Diverse evolutionary roots and mechanistic variations of the CRISPR–Cas systems. Science 353, aad5147 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR–Cas systems. Nat. Biotechnol. 31, 233–239 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR–Cas system. Cell 163, 759–771 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Deveau, H. et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190, 1390–1400 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602–607 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579–E2586 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cho, S. W., Kim, S., Kim, J. M. & Kim, J. S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31, 230–232 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gasiunas, G. et al. A catalogue of biochemically diverse CRISPR–Cas9 orthologs. Nat. Commun. 11, 5512 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aliaga Goltsman, D. S. et al. Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes. Nat. Commun. 13, 7602 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 57–65 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Makarova, K. S. & Koonin, E. V. Annotation and classification of CRISPR–Cas systems. Methods Mol. Biol. 1311, 47–75 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Teng, F. et al. Repurposing CRISPR–Cas12b for mammalian genome engineering. Cell Discov. 4, 63 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, W. Y. et al. The miniature CRISPR–Cas12m effector binds DNA to block transcription. Mol. Cell 82, 4487–4502 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Koonin, E. V., Makarova, K. S. & Zhang, F. Diversity, classification and evolution of CRISPR–Cas systems. Curr. Opin. Microbiol. 37, 67–78 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proc. Natl Acad. Sci. USA 120, e2308224120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Capdeville, N., Schindele, P. & Puchta, H. Getting better all the time—recent progress in the development of CRISPR/Cas-based tools for plant genome engineering. Curr. Opin. Biotechnol. 79, 102854 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, C. H., Lee, K. C. & Doudna, J. A. Applications of CRISPR–Cas enzymes in cancer therapeutics and detection. Trends Cancer 4, 499–512 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Donohoue, P. D., Barrangou, R. & May, A. P. Advances in industrial biotechnology using CRISPR–Cas systems. Trends Biotechnol. 36, 134–146 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kersulyte, D., Mukhopadhyay, A. K., Shirai, M., Nakazawa, T. & Berg, D. E. Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J. Bacteriol. 182, 5300–5308 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature 599, 692–696 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ton-Hoang, B. et al. Single-stranded DNA transposition is coupled to host replication. Cell 142, 398–408 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meers, C. et al. Transposon-encoded nucleases use guide RNAs to promote their selfish spread. Nature 622, 863–871 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Saito, M. et al. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature 620, 660–668 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jiang, K. et al. Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses. Sci. Adv. 9, eadk0171 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aravind, L., Makarova, K. S. & Koonin, E. V. Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28, 3417–3432 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Majorek, K. A. et al. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Nucleic Acids Res. 42, 4160–4179 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xiang, G. et al. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors. Nat. Biotechnol. 42, 745–757 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Makarova, K. S., Wolf, Y. I. & Koonin, E. V. in CRISPR: Biology and Applications (eds Barrangou, R., Sontheimer, E. J. & Marraffini, L. A.) Ch. 2 (Wiley, 2022).

  • Shmakov, S. et al. Diversity and evolution of class 2 CRISPR–Cas systems. Nat. Rev. Microbiol. 15, 169–182 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakagawa, R. et al. Cryo-EM structure of the transposon-associated TnpB enzyme. Nature 616, 390–397 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sasnauskas, G. et al. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 616, 384–389 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Swarts, D. C., van der Oost, J. & Jinek, M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR–Cas12a. Mol. Cell 66, 221–233 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, C. J., Adler, B. A. & Doudna, J. A. A naturally DNase-free CRISPR–Cas12c enzyme silences gene expression. Mol. Cell 82, 2148–2160 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wiegand, T. et al. TnpB homologues exapted from transposons are RNA-guided transcription factors. Nature 631, 439–448 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Turchiano, G. et al. Quantitative evaluation of chromosomal rearrangements in gene-edited human stem cells by CAST-seq. Cell Stem Cell 28, 1136–1147 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Takeda, S. N. et al. Structure of the miniature type V-F CRISPR–Cas effector enzyme. Mol. Cell 81, 558–570 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xiao, R., Li, Z., Wang, S., Han, R. & Chang, L. Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR–Cas12f nuclease. Nucleic Acids Res. 49, 4120–4128 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nety, S. P. et al. The transposon-encoded protein TnpB processes its own mRNA into ωRNA for guided nuclease activity. CRISPR J. 6, 232–242 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR–Cas systems. Mol. Cell 60, 385–397 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kurihara, N. et al. Structure of the type V-C CRISPR–Cas effector enzyme. Mol. Cell 82, 1865–1877 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, B. et al. Structural insights into target DNA recognition and cleavage by the CRISPR–Cas12c1 system. Nucleic Acids Res. 50, 11820–11833 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Z., Zhang, H., Xiao, R., Han, R. & Chang, L. Cryo-EM structure of the RNA-guided ribonuclease Cas12g. Nat. Chem. Biol. 17, 387–393 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Strecker, J. et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365, 48–53 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sun, A. et al. The compact Casπ (Cas12l) ‘bracelet’ provides a unique structural platform for DNA manipulation. Cell Res. 33, 229–244 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harrington, L. B. et al. A scoutRNA is required for some type V CRISPR–Cas systems. Mol. Cell 79, 416–424 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, J. J. et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566, 218–223 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liao, C. & Beisel, C. L. The tracrRNA in CRISPR biology and technologies. Annu. Rev. Genet. 55, 161–181 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fonfara, I., Richter, H., Bratovič, M., Le Rhun, A. & Charpentier, E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532, 517–521 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zetsche, B. et al. Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array. Nat. Biotechnol. 35, 31–34 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yan, W. X. et al. Functionally diverse type V CRISPR–Cas systems. Science 363, 88–91 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pausch, P. et al. CRISPR–CasΦ from huge phages is a hypercompact genome editor. Science 369, 333–337 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Al-Shayeb, B. et al. Diverse virus-encoded CRISPR–Cas systems include streamlined genome editors. Cell 185, 4574–4586 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, H., Li, Z., Xiao, R. & Chang, L. Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease. Nat. Struct. Mol. Biol. 27, 1069–1076 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karvelis, T. et al. PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res. 48, 5016–5023 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bravo, J. P. K. et al. RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2. Nature 613, 582–587 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abudayyeh, O. O. et al. RNA targeting with CRISPR–Cas13. Nature 550, 280–284 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao, P., Yang, H., Rajashankar, K. R., Huang, Z. & Patel, D. J. Type V CRISPR–Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res. 26, 901–913 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yamano, T. et al. Structural basis for the canonical and non-canonical PAM recognition by CRISPR–Cpf1. Mol. Cell 67, 633–645 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xiao, R. et al. Structural basis of target DNA recognition by CRISPR–Cas12k for RNA-guided DNA transposition. Mol. Cell 81, 4457–4466 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Swarts, D. C. et al. The evolutionary journey of Argonaute proteins. Nat. Struct. Mol. Biol. 21, 743–753 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hegge, J. W., Swarts, D. C. & van der Oost, J. Prokaryotic Argonaute proteins: novel genome-editing tools? Nat. Rev. Microbiol. 16, 5–11 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Swarts, D. C. Making the cut(s): how Cas12a cleaves target and non-target DNA. Biochem. Soc. Trans. 47, 1499–1510 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Selkova, P. et al. Position of Deltaproteobacteria Cas12e nuclease cleavage sites depends on spacer length of guide RNA. RNA Biol. 17, 1472–1479 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lei, C. et al. The CCTL (Cpf1-assisted cutting and Taq DNA ligase-assisted ligation) method for efficient editing of large DNA constructs in vitro. Nucleic Acids Res. 45, e74 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Strecker, J. et al. Engineering of CRISPR–Cas12b for human genome editing. Nat. Commun. 10, 212 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, X. et al. Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2. Nat. Commun. 11, 5241 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, J. S. et al. CRISPR–Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harrington, L. B. et al. Programmed DNA destruction by miniature CRISPR–Cas14 enzymes. Science 362, 839–842 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, L. et al. HOLMESv2: a CRISPR–Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth. Biol. 8, 2228–2237 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Swarts, D. C. & Jinek, M. Mechanistic insights into the cis– and trans-acting DNase activities of Cas12a. Mol. Cell 73, 589–600 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marino, N. D., Pinilla-Redondo, R. & Bondy-Denomy, J. CRISPR–Cas12a targeting of ssDNA plays no detectable role in immunity. Nucleic Acids Res. 50, 6414–6422 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dmytrenko, O. et al. Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA. Nature 613, 588–594 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wendt, K. E., Ungerer, J., Cobb, R. E., Zhao, H. & Pakrasi, H. B. CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973. Micro. Cell Fact. 15, 115 (2016).

    Article 

    Google Scholar
     

  • Jiang, Y. et al. CRISPR–Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat. Commun. 8, 15179 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Y. et al. Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems. Nat. Commun. 12, 1944 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Naduthodi, M. I. S. et al. CRISPR–Cas ribonucleoprotein mediated homology-directed repair for efficient targeted genome editing in microalgae Nannochloropsis oceanica IMET1. Biotechnol. Biofuels 12, 66 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wrighton, P. J. et al. Chemically modified AsCas12a guide RNAs improve lipid nanoparticle–mediated in vivo gene editing in different tissues. Presented at The American Society of Gene and Cell Therapy (ASGCT) Annual Meeting, May 7–11 (2024).

  • Sousa, P. et al. Preclinical development of EDIT301, an autologous cell therapy comprising AsCas12a-RNP modified mobilized peripheral blood-CD34+ cells for the potential treatment of transfusion dependent β thalassemia. Blood 138, 1858 (2021).

    Article 

    Google Scholar
     

  • Stein, R. A. Molecular scissors are making the cut…in clinical trials: treatments based on various genome editing technologies—CRISPR, TALEN, ZFN, and meganuclease technologies—are starting to reach patients. Genet. Eng. Biotechnol. N. 43, 36–38 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Hino, T. et al. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell 186, 4920–4935 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bigelyte, G. et al. Miniature type V-F CRISPR–Cas nucleases enable targeted DNA modification in cells. Nat. Commun. 12, 6191 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. Y. et al. Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus. Nat. Biotechnol. 40, 94–102 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, Z. et al. Programmed genome editing by a miniature CRISPR–Cas12f nuclease. Nat. Chem. Biol. 17, 1132–1138 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xu, X. et al. Engineered miniature CRISPR–Cas system for mammalian genome regulation and editing. Mol. Cell 81, 4333–4345 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, W. et al. Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors. Mol. Cell 83, 2768–2780 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, Y. et al. Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease. Cell Rep. 40, 111418 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tou, C. J., Orr, B. & Kleinstiver, B. P. Precise cut-and-paste DNA insertion using engineered type V-K CRISPR-associated transposases. Nat. Biotechnol. 41, 968–979 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, H. et al. An engineered xCas12i with high activity, high specificity, and broad PAM range. Protein Cell 14, 538–543 (2023).

    PubMed 

    Google Scholar
     

  • Chen, Y. et al. Synergistic engineering of CRISPR–Cas nucleases enables robust mammalian genome editing. Innovation 3, 100264 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Slaymaker, I. M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84–88 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kleinstiver, B. P. et al. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, H. et al. Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity. BMC Biol. 20, 91 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleinstiver, B. P. et al. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat. Biotechnol. 37, 276–282 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao, L. et al. Engineered Cpf1 variants with altered PAM specificities. Nat. Biotechnol. 35, 789–792 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tóth, E. et al. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res. 48, 3722–3733 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. Y. et al. Hypercompact adenine base editors based on transposase B guided by engineered RNA. Nat. Chem. Biol. 18, 1005–1013 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ma, E. et al. Improved genome editing by an engineered CRISPR–Cas12a. Nucleic Acids Res. 50, 12689–12701 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, T. et al. An engineered hypercompact CRISPR–Cas12f system with boosted gene-editing activity. Nat. Chem. Biol. 19, 1384–1393 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Z. et al. Engineering a transposon-associated TnpB–ωRNA system for efficient gene editing and phenotypic correction of a tyrosinaemia mouse model. Nat. Commun. 15, 831 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marquart, K. F. et al. Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs. Nat. Methods https://doi.org/10.1038/s41592-024-02418-z (2024).

  • Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parameshwaran, H. P. et al. The bridge helix of Cas12a imparts selectivity in cis-DNA cleavage and regulates trans-DNA cleavage. FEBS Lett. 595, 892–912 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yamano, T. et al. Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell 165, 949–962 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, X. et al. Base editing with a Cpf1–cytidine deaminase fusion. Nat. Biotechnol. 36, 324–327 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, X. et al. Cas12a base editors induce efficient and specific editing with low DNA damage response. Cell Rep. 31, 107723 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Certo, M. T. et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat. Methods 8, 671–676 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, W. Y., Lebbink, J. H. G., Kanaar, R., Geijsen, N. & van der Oost, J. Genome editing by natural and engineered CRISPR-associated nucleases. Nat. Chem. Biol. 14, 642–651 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, Y. B. et al. A novel mechanistic framework for precise sequence replacement using reverse transcriptase and diverse CRISPR–Cas systems. Preprint at bioRxiv https://doi.org/10.1101/2022.12.13.520319 (2022).

  • Liang, R. et al. Prime editing using CRISPR–Cas12a and circular RNAs in human cells. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-02095-x (2024).

  • Liu, B. et al. A split prime editor with untethered reverse transcriptase and circular RNA template. Nat. Biotechnol. 40, 1388–1393 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meliawati, M., Schilling, C. & Schmid, J. Recent advances of Cas12a applications in bacteria. Appl. Microbiol. Biotechnol. 105, 2981–2990 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, Y. et al. CAMERS-B: CRISPR/Cpf1 assisted multiple-genes editing and regulation system for Bacillus subtilis. Biotechnol. Bioeng. 117, 1817–1825 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schilling, C., Koffas, M. A. G., Sieber, V. & Schmid, J. Novel prokaryotic CRISPR–Cas12a-based tool for programmable transcriptional activation and repression. ACS Synth. Biol. 9, 3353–3363 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tak, Y. E. et al. Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors. Nat. Methods 14, 1163–1166 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kong, X. et al. Engineered CRISPR–OsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing. Nat. Commun. 14, 2046 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liang, M. et al. Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach. Nucleic Acids Res. 50, 3581–3592 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Enghiad, B. et al. Cas12a-assisted precise targeted cloning using in vivo Cre–lox recombination. Nat. Commun. 12, 1171 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Broughton, J. P. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38, 870–874 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, S. Y. et al. CRISPR–Cas12a-assisted nucleic acid detection. Cell Discov. 4, 20 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, S. Y. et al. CRISPR–Cas12a has both cis– and trans-cleavage activities on single-stranded DNA. Cell Res. 28, 491–493 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kaminski, M. M., Abudayyeh, O. O., Gootenberg, J. S., Zhang, F. & Collins, J. J. CRISPR-based diagnostics. Nat. Biomed. Eng. 5, 643–656 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Teng, F. et al. CDetection: CRISPR–Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol. 20, 132 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Z. & Zhong, C. Cas12c-DETECTOR: a specific and sensitive Cas12c-based DNA detection platform. Int. J. Biol. Macromol. 193, 441–449 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rananaware, S. R. et al. Programmable RNA detection with CRISPR–Cas12a. Nat. Commun. 14, 5409 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhou, S. et al. CRISPR/Cas12a-drived fluorescent and electrochemical signal-off/on dual-mode biosensors for ultrasensitive detection of EGFR 19del mutation. Sensor Actuat. B Chem. 392, 134034 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Klompe, S. E., Vo, P. L. H., Halpin-Healy, T. S. & Sternberg, S. H. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature 571, 219–225 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Peters, J. E., Makarova, K. S., Shmakov, S. & Koonin, E. V. Recruitment of CRISPR–Cas systems by Tn7-like transposons. Proc. Natl Acad. Sci. USA 114, E7358–E7366 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, J. U. et al. Structures of the holo CRISPR RNA-guided transposon integration complex. Nature 613, 775–782 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Querques, I., Schmitz, M., Oberli, S., Chanez, C. & Jinek, M. Target site selection and remodelling by type V CRISPR-transposon systems. Nature 599, 497–502 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. Uncovering the functional diversity of rare CRISPR–Cas systems with deep terascale clustering. Science 382, eadi1910 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durrant, M. G. et al. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat. Biotechnol. 41, 488–499 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, F. et al. Multiplexed base editing through Cas12a variant-mediated cytosine and adenine base editors. Commun. Biol. 5, 1163 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vialetto, E. et al. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res. 52, 6079–6091 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ding, X. et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR–Cas12a assay. Nat. Commun. 11, 4711 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, J. Y. & Doudna, J. A. CRISPR technology: a decade of genome editing is only the beginning. Science 379, eadd8643 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xin, C. et al. Comprehensive assessment of miniature CRISPR–Cas12f nucleases for gene disruption. Nat. Commun. 13, 5623 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, S. et al. Payload distribution and capacity of mRNA lipid nanoparticles. Nat. Commun. 13, 5561 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Villiger, L. et al. CRISPR technologies for genome, epigenome and transcriptome editing. Nat. Rev. Mol. Cell Biol. 25, 464–487 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wong, C. UK first to approve CRISPR treatment for diseases: what you need to know. Nature 623, 676–677 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Longhurst, H. J. et al. CRISPR–Cas9 in vivo gene editing of KLKB1 for hereditary angioedema. N. Engl. J. Med. 390, 432–441 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • O’Leary, K. Gene-editing breakthrough for a rare hereditary disorder. Nat. Med. https://doi.org/10.1038/d41591-024-00008-2 (2024).

  • Chew, W. L. Immunity to CRISPR Cas9 and Cas12a therapeutics. Wiley Interdiscip. Rev. Syst. Biol. Med. 10, e1408 (2018).

  • Wagner, D. L. et al. High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population. Nat. Med. 25, 242–248 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ferdosi, S. R. et al. Multifunctional CRISPR–Cas9 with engineered immunosilenced human T cell epitopes. Nat. Commun. 10, 1842 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burstein, D. et al. New CRISPR–Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yang, H. & Patel, D. J. CasX: a new and small CRISPR gene-editing protein. Cell Res. 29, 345–346 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Carabias, A. et al. Structure of the mini-RNA-guided endonuclease CRISPR–Cas12j3. Nat. Commun. 12, 4476 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, J. U. et al. Structural basis for target site selection in RNA-guided DNA transposition systems. Science 373, 768–774 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Urbaitis, T. et al. A new family of CRISPR-type V nucleases with C-rich PAM recognition. EMBO Rep. 23, e55481 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



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