Assessing and engineering the IscBRNA system for programmed genome editing – Nature.com

Kapitonov, V. V., Makarova, K. S. & Koonin, E. V. ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs. J. Bacteriol. 198, 797807 (2015).

Article PubMed Google Scholar

Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 5765 (2021).

Article CAS PubMed PubMed Central Google Scholar

Meers, C. et al. Transposon-encoded nucleases use guide RNAs to promote their selfish spread. Nature 622, 863871 (2023).

Article CAS PubMed Google Scholar

Schuler, G., Hu, C. & Ke, A. Structural basis for RNA-guided DNA cleavage by IscBRNA and mechanistic comparison with Cas9. Science 376, 14761481 (2022).

Article CAS PubMed PubMed Central Google Scholar

Kato, K. et al. Structure of the IscBRNA ribonucleoprotein complex, the likely ancestor of CRISPRCas9. Nat. Commun. 13, 6719 (2022).

Article CAS PubMed PubMed Central Google Scholar

Hirano, S. et al. Structure of the OMEGA nickase IsrB in complex with RNA and target DNA. Nature 610, 575581 (2022).

Article CAS PubMed PubMed Central Google Scholar

Lino, C. A., Harper, J. C., Carney, J. P. & Timlin, J. A. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv. 25, 12341257 (2018).

Article CAS PubMed PubMed Central Google Scholar

Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M. & Joung, J. K. Improving CRISPRCas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279284 (2014).

Article CAS PubMed PubMed Central Google Scholar

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, 420424 (2016).

Article CAS PubMed PubMed Central Google Scholar

Nishida, K. et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729 (2016).

Article PubMed Google Scholar

Gaudelli, N. M. et al. Programmable base editing of AT to GC in genomic DNA without DNA cleavage. Nature 551, 464471 (2017).

Article CAS PubMed PubMed Central Google Scholar

Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPRCas nucleases. Nat. Biotechnol. 33, 187197 (2015).

Article CAS PubMed Google Scholar

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 6267 (2014).

Article CAS PubMed PubMed Central Google Scholar

Xiao, Y. et al. Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPRCas system. Cell 170, 4860 (2017).

Article CAS PubMed PubMed Central Google Scholar

Hu, C. et al. Allosteric control of type I-A CRISPRCas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Mol. Cell 82, 27542768 (2022).

Article CAS PubMed PubMed Central Google Scholar

Nishimasu, H. et al. Engineered CRISPRCas9 nuclease with expanded targeting space. Science 361, 12591262 (2018).

Article CAS PubMed PubMed Central Google Scholar

Walton, R. T., Christie, K. A., Whittaker, M. N. & Kleinstiver, B. P. Unconstrained genome targeting with near-PAMless engineered CRISPRCas9 variants. Science 368, 290296 (2020).

Article CAS PubMed PubMed Central Google Scholar

Nakagawa, R. et al. Engineered Campylobacter jejuni Cas9 variant with enhanced activity and broader targeting range. Commun. Biol. 5, 211 (2022).

Article CAS PubMed PubMed Central Google Scholar

Kleinstiver, B. P. et al. Engineered CRISPRCas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat. Biotechnol. 37, 276282 (2019).

Article CAS PubMed PubMed Central Google Scholar

Strecker, J. et al. Engineering of CRISPRCas12b for human genome editing. Nat. Commun. 10, 212 (2019).

Article CAS PubMed PubMed Central Google Scholar

McGaw, C. et al. Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing. Nat. Commun. 13, 2833 (2022).

Article CAS PubMed PubMed Central Google Scholar

Xu, X. et al. Engineered miniature CRISPRCas system for mammalian genome regulation and editing. Mol. Cell 81, 43334345 (2021).

Article CAS PubMed Google Scholar

Wu, T. et al. An engineered hypercompact CRISPRCas12f system with boosted gene-editing activity. Nat. Chem. Biol. 19, 13841393 (2023).

Article CAS PubMed PubMed Central Google Scholar

Kong, X. et al. Engineered CRISPROsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing. Nat. Commun. 14, 2046 (2023).

Article CAS PubMed PubMed Central Google Scholar

Saito, M. et al. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature 620, 660668 (2023).

Article CAS PubMed PubMed Central Google Scholar

Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224226 (2019).

Article CAS PubMed PubMed Central Google Scholar

Dang, Y. et al. Optimizing sgRNA structure to improve CRISPRCas9 knockout efficiency. Genome Biol. 16, 280 (2015).

Article PubMed PubMed Central Google Scholar

Moon, S. B., Kim, D. Y., Ko, J.-H., Kim, J.-S. & Kim, Y.-S. Improving CRISPR genome editing by engineering guide RNAs. Trends Biotechnol. 37, 870881 (2019).

Article CAS PubMed 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, 94102 (2022).

Article CAS PubMed Google Scholar

Srisawat, C., Goldstein, I. J. & Engelke, D. R. Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res. 29, E4 (2001).

Article CAS PubMed PubMed Central Google Scholar

Steckelberg, A. L. et al. A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. Proc. Natl Acad. Sci. USA 115, 64046409 (2018).

Article CAS PubMed PubMed Central Google Scholar

Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 13551358 (2010).

Article CAS PubMed PubMed Central Google Scholar

Han, D. et al. Development of miniature base editors using engineered IscB nickase. Nat. Methods 20, 10291036 (2023).

Article CAS PubMed Google Scholar

Harrington, L. B. et al. Programmed DNA destruction by miniature CRISPRCas14 enzymes. Science 362, 839842 (2018).

Article CAS PubMed PubMed Central Google Scholar

Karvelis, T. et al. PAM recognition by miniature CRISPRCas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res. 48, 50165023 (2020).

Article CAS PubMed PubMed Central Google Scholar

Wu, W. Y. et al. The miniature CRISPRCas12m effector binds DNA to block transcription. Mol. Cell 82, 44874502 (2022).

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, 27682780 (2023).

Article CAS PubMed Google Scholar

Richter, M. F. et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38, 883891 (2020).

Article CAS PubMed PubMed Central Google Scholar

Rees, H. A., Wilson, C., Doman, J. L. & Liu, D. R. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci. Adv. 5, eaax5717 (2019).

Article PubMed PubMed Central Google Scholar

Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPRCas9 off-target effects in human cells. Nat. Methods 12, 237243 (2015).

Article CAS PubMed Google Scholar

Tsai, S. Q. et al. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPRCas9 nuclease off-targets. Nat. Methods 14, 607614 (2017).

Article CAS PubMed PubMed Central Google Scholar

Petri, K. et al. Global-scale CRISPR gene editor specificity profiling by ONE-seq identifies population-specific, variant off-target effects. Preprint at bioRxiv https://doi.org/10.1101/2021.04.05.438458 (2021).

Kleinstiver, B. P. et al. Genome-wide specificities of CRISPRCas Cpf1 nucleases in human cells. Nat. Biotechnol. 34, 869874 (2016).

Article CAS PubMed PubMed Central Google Scholar

Bae, S., Park, J. & Kim, J. S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 14731475 (2014).

Article CAS PubMed PubMed Central Google Scholar

Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 60976100 (1990).

Article CAS PubMed PubMed Central Google Scholar

Sternberg, S. H., LaFrance, B., Kaplan, M. & Doudna, J. A. Conformational control of DNA target cleavage by CRISPRCas9. Nature 527, 110113 (2015).

Article CAS PubMed PubMed Central Google Scholar

Chen, J. S. et al. Enhanced proofreading governs CRISPRCas9 targeting accuracy. Nature 550, 407410 (2017).

Article CAS PubMed PubMed Central Google Scholar

Bravo, J. P. K. et al. Structural basis for mismatch surveillance by CRISPRCas9. Nature 603, 343347 (2022).

Article CAS PubMed PubMed Central Google Scholar

Russ, W. P. et al. An evolution-based model for designing chorismate mutase enzymes. Science 369, 440445 (2020).

Article CAS PubMed Google Scholar

Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature 599, 692696 (2021).

Article CAS PubMed PubMed Central Google Scholar

Geurts, A. M. et al. Gene transfer into genomes of human cells by the Sleeping Beauty transposon system. Mol. Ther. 8, 108117 (2003).

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Assessing and engineering the IscBRNA system for programmed genome editing - Nature.com