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RNA-guided editing of bacterial genomes using CRISPR-Cas systems
Open accessAbstract
Here we use the clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 endonuclease complexed with dual-RNAs to introduce precise mutations in the genomes of Streptococcus pneumoniae and Escherichia coli. The approach relies on dual-RNA:Cas9-directed cleavage at the targeted genomic site to kill unmutated cells and circumvents the need for selectable markers or counter-selection systems. We reprogram dual-RNA:Cas9 specificity by changing the sequence of short CRISPR RNA (crRNA) to make single- and multinucleotide changes carried on editing templates. Simultaneous use of two crRNAs enables multiplex mutagenesis. In S. pneumoniae, nearly 100% of cells that were recovered using our approach contained the desired mutation, and in E. coli, 65% that were recovered contained the mutation, when the approach was used in combination with recombineering. We exhaustively analyze dual-RNA:Cas9 target requirements to define the range of targetable sequences and show strategies for editing sites that do not meet these requirements, suggesting the versatility of this technique for bacterial genome engineering.
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“As an example, the most common Cas9 system, SpCas9, recognises NGG motifs and therefore only sequences adjacent to that motif can be targeted [60].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [60]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“CRISPR systems might be an alternative or a tool to use together with conventional antibiotics, either by disabling antibiotic-resistance genes or by developing toxicity in bacteria through the cleavage of crucial domains of their genome, exerting a bactericidal effect [60].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [60]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
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“In early 2013, Jiang et al. used the CRISPR-Cas9 system to induce targeted mutations (insertions, deletions, and single-nucleotide substitutions) in the genome of Streptococcus pneumoniae and E. coli strains [60].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [60]
In the citing paper
“The type II CRISPR/Cas9 system has been exploited for high-efficiency gene editing in model microorganisms such as E. coli (Jiang et al., 2015), S. cerevisiae (DiCarlo et al., 2013), and Streptococcus pneumoniae (Jiang et al., 2013).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Jiang et al., 2013
In the citing paper
“Collectively, these studies indicate that although each base within the 20 nt guide sequence contributes to overall specificity”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [93]
In the citing paper
“multiple mismatches between the guide RNA and its complementary target DNA sequence can be tolerated depending on the quantity, position, and base identity of mismatches [87,90,91,93], all of which contribute to potential off-target activity.”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [93]
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Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Self-citationEnzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 10,088
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210
CRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208507109 · Cited by 2,769
CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III
Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., & Charpentier, E. (2011) · Nature · doi:10.1038/nature09886 · Cited by 2,563
CRISPR/Cas, the Immune System of Bacteria and Archaea
Horvath, P., & Barrangou, R. (2010) · Science · doi:10.1126/science.1179555 · Cited by 2,471
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
Brouns, S. J. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J. H., Snijders, A. P. L., Dickman, M. J., Makarova, K. S., Koonin, E. V., & van der Oost, J. (2008) · Science · doi:10.1126/science.1159689 · Cited by 2,460
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Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
Self-citationDevelopment and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundCpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Self-citationCRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696
“Recently, several groups have shown that a modified type II CRISPR (Clustered Regularly Interspaced Palindromic Repeats) system can be targeted to DNA using RNA, enabling genetic editing of any region of the genome in a variety of organisms (Cho et al., 2013; Cong et al., 2013; Dicarlo et al., 2013; Gratz et al., 2013…”
BackgroundInfluentialZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013) · Trends in Biotechnology · doi:10.1016/j.tibtech.2013.04.004 · Cited by 3,820
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495
Self-citationDouble nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
CRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153
High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects
Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Zheng, Z., & Joung, J. K. (2016) · Nature · doi:10.1038/nature16526 · Cited by 2,673
Rationally engineered Cas9 nucleases with improved specificity
Slaymaker, I. M., Gao, L., Zetsche, B., Scott, D. A., Yan, W. X., & Zhang, F. (2016) · Science · doi:10.1126/science.aad5227 · Cited by 2,414
Self-citationGUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268
Targeted genome modification of crop plants using a CRISPR-Cas system
Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J. J., Qiu, J.-L., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2650 · Cited by 1,810
CRISPR–Cas9 Structures and Mechanisms
Jiang, F., & Doudna, J. A. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010822 · Cited by 2,029
Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
Cho, S. W., Kim, S., Kim, J. M., & Kim, J.-S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2507 · Cited by 1,863
Kim, S., Kim, D., Cho, S. W., Kim, J., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.171322.113 · Cited by 1,856
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,822
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752
Li, H., Yang, Y., Hong, W., Huang, M., Wu, M., & Zhao, X. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0089-y · Cited by 1,829
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P. W., Li, Z., Peterson, R. T., Yeh, J.-R. J., et al. (2015) · Nature · doi:10.1038/nature14592 · Cited by 1,624
Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation
Doench, J. G., Hartenian, E., Graham, D. B., Tothova, Z., Hegde, M., Smith, I., Sullender, M., Ebert, B. L., Xavier, R. J., & Root, D. E. (2014) · Nature Biotechnology · doi:10.1038/nbt.3026 · Cited by 1,617
Yang, H., Wang, H., Shivalila, C. S., Cheng, A. W., Shi, L., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.022 · Cited by 1,596
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J., & Church, G. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt135 · Cited by 1,566
Li, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,533
Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487
Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems
Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K. Y., et al. (2016) · Science · doi:10.1126/science.aaf8729 · Cited by 1,349
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.162339.113 · Cited by 1,356
Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system
Jiang, Y., Chen, B., Duan, C., Sun, B., Yang, J., & Yang, S. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.04023-14 · Cited by 1,362
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
Anders, C., Niewoehner, O., Duerst, A., & Jinek, M. (2014) · Nature · doi:10.1038/nature13579 · Cited by 1,323
Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
Jao, L.-E., Wente, S. R., & Chen, W. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308335110 · Cited by 1,311
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.008 · Cited by 1,209
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
Montague, T. G., Cruz, J. M. B. S., Gagnon, J. A., Church, G. M., & Valen, E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku410 · Cited by 1,246
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants
Walton, R. T., Christie, K. A., Whittaker, M. N., & Kleinstiver, B. P. (2020) · Science · doi:10.1126/science.aba8853 · Cited by 1,233
CRISPR interference (CRISPRi) for sequence-specific control of gene expression
Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.132 · Cited by 1,241
Cas9 as a versatile tool for engineering biology
Mali, P., Esvelt, K. M., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2649 · Cited by 1,197
The CRISPR/Cas9 system for plant genome editing and beyond
Bortesi, L., & Fischer, R. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.12.006 · Cited by 1,289
Delivering CRISPR: a review of the challenges and approaches
Lino, C. A., Harper, J. C., Carney, J. P., & Timlin, J. A. (2018) · Drug Delivery · doi:10.1080/10717544.2018.1474964 · Cited by 1,185
A guide to genome engineering with programmable nucleases
Kim, S., & Kim, J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3686 · Cited by 1,216
CRISPR/Cas9 in Genome Editing and Beyond
Wang, H., Russa, M. F. L., & Qi, L. S. (2016) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060815-014607 · Cited by 1,213
Maruyama, T., Dougan, S. K., Truttmann, M. C., Bilate, A. M., Ingram, J. R., & Ploegh, H. L. (2015) · Nature Biotechnology · doi:10.1038/nbt.3190 · Cited by 1,137
Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt520 · Cited by 1,145
Digenome-seq: Genome-wide profiling of CRISPR-cas9 off-target effects in human cells
Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H. R., Hwang, J., Kim, J.-I., & Kim, J.-S. (2015) · Nature Methods · doi:10.1038/nmeth.3284 · Cited by 992
Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials
Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., Fischetti, V. A., & Marraffini, L. A. (2014) · Nature Biotechnology · doi:10.1038/nbt.3043 · Cited by 986
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,037
Sharma, S. J., Mohler, J. L., Mahajan, S. D., Schwartz, S. A., Bruggemann, L., & Aalinkeel, R. (2023) · Microorganisms · doi:10.3390/microorganisms11061614 · Cited by 1,150
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944
Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering
Wright, A. V., Nuñez, J. K., & Doudna, J. A. (2016) · Cell · doi:10.1016/j.cell.2015.12.035 · Cited by 989
Applications of CRISPR technologies in research and beyond
Barrangou, R., & Doudna, J. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3659 · Cited by 1,005
Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination
Dickinson, D. J., Ward, J. D., Reiner, D. J., & Goldstein, B. (2013) · Nature Methods · doi:10.1038/nmeth.2641 · Cited by 956
Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9
Paquet, D., Kwart, D., Chen, A., Sproul, A., Jacob, S., Teo, S., Olsen, K. M., Gregg, A., Noggle, S., & Tessier-Lavigne, M. (2016) · Nature · doi:10.1038/nature17664 · Cited by 951
A brief history of synthetic biology
Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3239 · Cited by 988
CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity
Barrangou, R., & Marraffini, L. A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.011 · Cited by 832
Heritable genome editing in C. elegans via a CRISPR-Cas9 system
Friedland, A. E., Tzur, Y. B., Esvelt, K. M., Colaiácovo, M. P., Church, G. M., & Calarco, J. A. (2013) · Nature Methods · doi:10.1038/nmeth.2532 · Cited by 899
E-CRISP: fast CRISPR target site identification
Heigwer, F., Kerr, G., & Boutros, M. (2014) · Nature Methods · doi:10.1038/nmeth.2812 · Cited by 884
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832
Concerning RNA-guided gene drives for the alteration of wild populations
Esvelt, K. M., Smidler, A. L., Catteruccia, F., & Church, G. M. (2014) · eLife · doi:10.7554/elife.03401 · Cited by 889
Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases
Citorik, R. J., Mimee, M., & Lu, T. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.3011 · Cited by 808
CRISPR-Cas immunity in prokaryotes
Marraffini, L. A. (2015) · Nature · doi:10.1038/nature15386 · Cited by 860
Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects
Shen, B., Zhang, W., Zhang, J., Zhou, J., Wang, J., Chen, L., Wang, L., Hodgkins, A., Iyer, V., Huang, X., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2857 · Cited by 769
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777
RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System
Xie, K., & Yang, Y. (2013) · Molecular Plant · doi:10.1093/mp/sst119 · Cited by 822
CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants
Yang, L., Lü, L., Liu, H., Li, S., Feng, X., & Chen, L. (2014) · Molecular Plant · doi:10.1093/mp/ssu044 · Cited by 815
Arribere, J. A., Bell, R. T., Fu, B. X. H., Artiles, K. L., Hartman, P. S., & Fire, A. Z. (2014) · Genetics · doi:10.1534/genetics.114.169730 · Cited by 761
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2681 · Cited by 786
Genome editing in rice and wheat using the CRISPR/Cas system
Shan, Q., Wang, Y., Li, J., & Gao, C. (2014) · Nature Protocols · doi:10.1038/nprot.2014.157 · Cited by 775
Cheng, A. W., Wang, H., Yang, H., Shi, L., Yarden Katz, A., Theunissen, T. W., Rangarajan, S., Shivalila, C., Dadon, D. B., & Jaenisch, R. (2013) · Cell Research · doi:10.1038/cr.2013.122 · Cited by 768
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Wang, Y., Xue, P., Cao, M., Yu, T., Lane, S., & Zhao, H. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00260 · Cited by 745
Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection
Liang, X., Potter, J., Kumar, S., Zou, Y., Quintanilla, R., Sridharan, M., Carte, J., Chen, W., Roark, N., Ranganathan, S., et al. (2015) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2015.04.024 · Cited by 733
Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells
Kim, D., Kim, J., Hur, J. K., Been, K. W., Yoon, S.-H., & Kim, J.-S. (2016) · Nature Biotechnology · doi:10.1038/nbt.3609 · Cited by 731
Fauser, F., Schiml, S., & Puchta, H. (2014) · The Plant Journal · doi:10.1111/tpj.12554 · Cited by 733
Unravelling the structural and mechanistic basis of CRISPR–Cas systems
John van der, O. O. S. T., Westra, E. R., Jackson, R. N., & Wiedenheft, B. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3279 · Cited by 740
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
Frock, R. L., Hu, J., Meyers, R. M., Ho, Y.-J., Kii, E., & Alt, F. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3101 · Cited by 673
CRISPR/Cas9 for genome editing: progress, implications and challenges
Zhang, F., Wen, Y., & Guo, X. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu125 · Cited by 720
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
Paddon, C. J., & Keasling, J. D. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3240 · Cited by 675
Functional annotation of native enhancers with a Cas9–histone demethylase fusion
Kearns, N. A., Pham, H., Tabak, B., Genga, R. M., Silverstein, N. J., Garber, M., & Maehr, R. (2015) · Nature Methods · doi:10.1038/nmeth.3325 · Cited by 656
Lin, Y., Cradick, T. J., Brown, M. T., Deshmukh, H., Ranjan, P., Sarode, N., Wile, B. M., Vertino, P. M., Stewart, F. J., & Bao, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku402 · Cited by 634
Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA
Ramakrishna, S., Kwaku Dad, A.-B., Beloor, J., Gopalappa, R., Lee, S.-K., & Kim, H. (2014) · Genome Research · doi:10.1101/gr.171264.113 · Cited by 655
Heritable gene targeting in the mouse and rat using a CRISPR-Cas system
Li, D., Qiu, Z., Shao, Y., Chen, Y., Guan, Y., Liu, M., Li, Y., Wang, L., Wang, L., Lu, X., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2661 · Cited by 653
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Topkar, V. V., Zheng, Z., & Joung, J. K. (2015) · Nature Biotechnology · doi:10.1038/nbt.3404 · Cited by 611
CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity
Cradick, T. J., Fine, E. J., Antico, C. J., & Bao, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt714 · Cited by 590
Belhaj, K., Chaparro‐Garcia, A., Kamoun, S., & Nekrasov, V. (2013) · Plant Methods · doi:10.1186/1746-4811-9-39 · Cited by 603
Lawrenson, T., Shorinola, O., Stacey, N., Li, C., Østergaard, L., Patron, N., Uauy, C., & Harwood, W. (2015) · Genome Biology · doi:10.1186/s13059-015-0826-7 · Cited by 551
Cobb, R. E., Wang, Y., & Zhao, H. (2014) · ACS Synthetic Biology · doi:10.1021/sb500351f · Cited by 579
A Cas9–guide RNA complex preorganized for target DNA recognition
Jiang, F., Zhou, K., Ma, L., Gressel, S., & Doudna, J. A. (2015) · Science · doi:10.1126/science.aab1452 · Cited by 562
Ishino, Y., Krupovic, M., & Forterre, P. (2018) · Journal of Bacteriology · doi:10.1128/jb.00580-17 · Cited by 558
Industrial biomanufacturing: The future of chemical production
Clomburg, J. M., Crumbley, A. M., & González, R. (2017) · Science · doi:10.1126/science.aag0804 · Cited by 565
Genome Engineering with Targetable Nucleases
Carroll, D. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035418 · Cited by 568
Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9322 · Cited by 543
Editing plant genomes with CRISPR/Cas9
Belhaj, K., Chaparro‐Garcia, A., Kamoun, S., Patron, N. J., & Nekrasov, V. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.11.007 · Cited by 559
Genome Engineering Using CRISPR-Cas9 System
Cong, L., & Zhang, F. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1862-1_10 · Cited by 536
Classification and evolution of type II CRISPR-Cas systems
Chylinski, K., Makarova, K. S., Charpentier, E., & Koonin, E. V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku241 · Cited by 498
Fundamentals, Applications, and Future Directions of Bioelectrocatalysis
Chen, H., Simoska, O., Lim, K., Grattieri, M., Yuan, M., Dong, F., Lee, Y. S., Beaver, K., Weliwatte, N. S., Gaffney, E. M., et al. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.0c00472 · Cited by 510
Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria
Yosef, I., Manor, M., Kiro, R., & Qimron, U. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1500107112 · Cited by 483
CRISPR-Cas: biology, mechanisms and relevance
Hille, F., & Charpentier, E. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0496 · Cited by 442
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing
Li, Y., Lin, Z., Huang, C., Zhang, Y., Wang, Z., Ya-jie Tang, A., Chen, T., & Zhao, X. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.06.006 · Cited by 480
Liew, F., Martin, M. E., Tappel, R. C., Heijstra, B. D., Mihalcea, C., & Köpke, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00694 · Cited by 485
Synthetic biology to access and expand nature's chemical diversity
Smanski, M. J., Zhou, H. L., Claesen, J., Shen, B., Fischbach, M. A., & Voigt, C. A. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2015.24 · Cited by 487
Metadata
- Authors
- Jiang, W., Bikard, D., Cox, D., Zhang, F., & Marraffini, L. A.
- Affiliations
- Rockefeller University (US)
- Broad Institute (US)
- Corresponding author
- Bikard, David
- Marraffini, Luciano A
- Venue
- Nature Biotechnology
- Published
- 2013-01-29
- Volume
- 31
- Issue
- 3
- Pages
- 233-239
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3748948
- OpenAlex
- W2000046950
- Cited by
- 2,429
- References
- 51
- Citations by year
- 2026: 84 · 2025: 124 · 2024: 151 · 2023: 162 · 2022: 199 · 2021: 203 · 2020: 245 · 2019: 185 · 2018: 206 · 2017: 208 · 2016: 203 · 2015: 174 · 2014: 183 · 2013: 98
- FWCI
- 98.32
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- U.S. Public Health Service
- National Institute of Mental Health (DP1MH100706)
- National Institute of General Medical Sciences (T32GM007753)
- National Institute of Allergy and Infectious Diseases (DP2AI104556)
- National Center for Chronic Disease Prevention and Health Promotion (DP1‑MH100706)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas9, bacterial genome editing, Streptococcus pneumoniae, Escherichia coli, targeted mutagenesis, recombineering, genome editing
- MeSH terms
- Base Sequence, Endonucleases, Escherichia coli, Genetic Engineering, Molecular Sequence Data, Streptococcus pneumoniae, Mutagenesis, Site-Directed, Genome, Bacterial, DNA Cleavage, RNA, Small Untranslated
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