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Journal ArticleDOI

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

01 Nov 2013-Nucleic Acids Research (Oxford University Press)-Vol. 41, Iss: 20
TL;DR: Adaptations of the type II CRISPR/Cas system leading to successful expression of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.
Abstract: The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5' coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.
Citations
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Journal ArticleDOI
28 Nov 2014-Science
TL;DR: The power of the CRISPR-Cas9 technology to systematically analyze gene functions in mammalian cells, study genomic rearrangements and the progression of cancers or other diseases, and potentially correct genetic mutations responsible for inherited disorders is illustrated.
Abstract: The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.

4,774 citations

Journal ArticleDOI
TL;DR: A modified version of the CRISPR-Cas9 system has been developed to recruit heterologous domains that can regulate endogenous gene expression or label specific genomic loci in living cells, which will undoubtedly transform biological research and spur the development of novel molecular therapeutics for human disease.
Abstract: Targeted genome editing using engineered nucleases has rapidly gone from being a niche technology to a mainstream method used by many biological researchers. This widespread adoption has been largely fueled by the emergence of the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology, an important new approach for generating RNA-guided nucleases, such as Cas9, with customizable specificities. Genome editing mediated by these nucleases has been used to rapidly, easily and efficiently modify endogenous genes in a wide variety of biomedically important cell types and in organisms that have traditionally been challenging to manipulate genetically. Furthermore, a modified version of the CRISPR-Cas9 system has been developed to recruit heterologous domains that can regulate endogenous gene expression or label specific genomic loci in living cells. Although the genome-wide specificities of CRISPR-Cas9 systems remain to be fully defined, the power of these systems to perform targeted, highly efficient alterations of genome sequence and gene expression will undoubtedly transform biological research and spur the development of novel molecular therapeutics for human disease.

2,930 citations

Journal ArticleDOI
TL;DR: A robust CRISPR/Cas9 vector system, utilizing a plant codon optimized Cas9 gene, for convenient and high-efficiency multiplex genome editing in monocot and dicot plants and provides examples of loss-of-function gene mutations in T0 rice and Arabidopsis plants.

1,451 citations


Cites background or methods from "Demonstration of CRISPR/Cas9/sgRNA-..."

  • ...For Gibson Assembly cloning, home-made 23 isothermal in vitro recombination master mixture was prepared as previously described (Jiang et al., 2013a, 2013b)....

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  • ...CRISPR/Cas9 editing systems have enabled genomic targeting in many organisms, including plants (Cong et al., 2013; Jiang et al., 2013a, 2013b; Li et al., 2013; Mao et al., 2013; Miao et al., 2013; Shan et al., 2013b; Xie and Yang, 2013; Fauser et al., 2014; Zhang et al., 2014; Zhou et al., 2014)....

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  • ...…expression cassettes can be combined into a single T-DNA region, current plant CRISPR/Cas9 vector systems can only target one or few genomic sites (Jiang et al., 2013a, 2013b; Li et al., 2013; Mao et al., 2013; Shan et al., 2013a, 2013b; Xie and Yang, 2013; M Fauser et al., 2014; Feng et al.,…...

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Journal ArticleDOI
TL;DR: A toolkit that facilitates transient or stable expression of the CRISPR/Cas9 system in a variety of plant species, which will facilitate plant research, as it enables high efficiency generation of mutants bearing multiple gene mutations.
Abstract: To accelerate the application of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9) system to a variety of plant species, a toolkit with additional plant selectable markers, more gRNA modules, and easier methods for the assembly of one or more gRNA expression cassettes is required. We developed a CRISPR/Cas9 binary vector set based on the pGreen or pCAMBIA backbone, as well as a gRNA (guide RNA) module vector set, as a toolkit for multiplex genome editing in plants. This toolkit requires no restriction enzymes besides BsaI to generate final constructs harboring maize-codon optimized Cas9 and one or more gRNAs with high efficiency in as little as one cloning step. The toolkit was validated using maize protoplasts, transgenic maize lines, and transgenic Arabidopsis lines and was shown to exhibit high efficiency and specificity. More importantly, using this toolkit, targeted mutations of three Arabidopsis genes were detected in transgenic seedlings of the T1 generation. Moreover, the multiple-gene mutations could be inherited by the next generation. We developed a toolkit that facilitates transient or stable expression of the CRISPR/Cas9 system in a variety of plant species, which will facilitate plant research, as it enables high efficiency generation of mutants bearing multiple gene mutations.

1,021 citations


Cites background from "Demonstration of CRISPR/Cas9/sgRNA-..."

  • ...The CRISPR/Cas system has been harnessed to achieve efficient genome editing in a variety of organisms, including bacteria, yeast, plants, and animals, as well as human cell lines [12-27]....

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Journal ArticleDOI
TL;DR: The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (Cas9) system is described, a recently developed tool for the introduction of site-specific double-stranded DNA breaks and the strengths and weaknesses are highlighted.

948 citations


Cites background from "Demonstration of CRISPR/Cas9/sgRNA-..."

  • ...Subsequent work focused on additional crop species such as sorghum (Jiang et al., 2013b), wheat (Upadhyay et al., 2013; Wang et al., 2014b) andmaize (Liang et al., 2014)....

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  • ...…it was later shown that only the 8–12 nt at the 3′ end (the seed sequence) is needed for target site recognition and cleavage (Cong et al., 2013; Jiang et al., 2013a; Jinek et al., 2012), whereas multiple mismatches in the PAM-distal region can be tolerated, depending on the total number and…...

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  • ...…of CRISPR/Cas9 One of the few criticisms of the CRISPR/Cas9 technology is the relatively high frequency of off-target mutations reported in some of the earlier studies (Cong et al., 2013; Fu et al., 2013; Hsu et al., 2013; Jiang et al., 2013a; Mali et al., 2013; Pattanayak et al., 2013)....

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  • ...…under the control of diverse promoters, including those recognized by RNA polymerase II and III (Fauser et al., 2014; Feng et al., 2014; Gao et al., 2014; Jiang et al., 2013b; Mao et al., 2013; Miao et al., 2013; Sugano et al., 2014; Upadhyay et al., 2013; Zhang et al., 2014; Zhou et al., 2014)....

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References
More filters
Journal ArticleDOI
17 Aug 2012-Science
TL;DR: This study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.

12,865 citations


"Demonstration of CRISPR/Cas9/sgRNA-..." refers background or methods in this paper

  • ...Because it is reported that Cas9 nucleases cleave 3 nt upstream of the PAM sequence (27), it is likely that our ApaLI-mediated enrichment for GFP target site mutations may well have resulted in lack of recovery of a number of target region mutations....

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  • ...An important innovation was the development of single guide RNAs (sgRNAs) that are fusions of critical portions of tracrRNA with the ‘guide’ and PAM domains of crRNAs (27,29) (Figure 1)....

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  • ...The deletion is located in close proximity to the predicted cleavage site of the Cas9/sgRNA complex [3-bp downstream of PAM sequence (27)], indicating the association of the mutation with Cas9/sgRNA-directed DNA cleavage....

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  • ...Constructs for Cas9 and sgRNA gene expression in rice The S. pyogenes Cas9 (SpCas9) coding sequence from plasmid pMJ806 (Jinek et al., 2012, obtained from Addgene, http://www.addgene.org/) was PCR amplified with primers Cas9-F1 and Cas9-R1 (Supplementary Information) that contain restriction sites…...

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Journal ArticleDOI
15 Feb 2013-Science
TL;DR: The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage as discussed by the authors.
Abstract: Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

12,265 citations

01 Feb 2013
TL;DR: Two different type II CRISPR/Cas systems are engineered and it is demonstrated that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
Abstract: Genome Editing Clustered regularly interspaced short palindromic repeats (CRISPR) function as part of an adaptive immune system in a range of prokaryotes: Invading phage and plasmid DNA is targeted for cleavage by complementary CRISPR RNAs (crRNAs) bound to a CRISPR-associated endonuclease (see the Perspective by van der Oost). Cong et al. (p. 819, published online 3 January) and Mali et al. (p. 823, published online 3 January) adapted this defense system to function as a genome editing tool in eukaryotic cells. A bacterial genome defense system is adapted to function as a genome-editing tool in mammalian cells. [Also see Perspective by van der Oost] Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

10,746 citations


Additional excerpts

  • ...in bacteria (30,32), yeast (33), zebrafish (34–36), fruit fly (37) and human cells (28,29,38)]....

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Journal ArticleDOI
15 Feb 2013-Science
TL;DR: The type II bacterial CRISPR system is engineer to function with custom guide RNA (gRNA) in human cells to establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
Abstract: Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.

8,197 citations


"Demonstration of CRISPR/Cas9/sgRNA-..." refers background or methods in this paper

  • ...An important innovation was the development of single guide RNAs (sgRNAs) that are fusions of critical portions of tracrRNA with the ‘guide’ and PAM domains of crRNAs (27,29) (Figure 1)....

    [...]

  • ...The coding region of Cas9 was fused in frame with a 2XFLAG (GA TTACAAGGACGATGATGACAAGAAAGACTATA AAGATGACGATGATAAGCAT) at the 50 terminus immediately downstream of the ATG start codon and with a SV40 nuclear localization sequence (CCGAAGAAGAAG CGCAAGGTGTAA) at the 30 end of the gene (29)....

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  • ...The 50 end of the transcript contained a 20-bp target sequence (GCGCTTCAAGGTGCACAT GG) complementary to the target site in the 50 coding region of a nonfunctional GFP gene (see description later in the text) and was followed the sgRNA scaffold (GTTTT AGAGCTAGAAATAGCAAGTTAAAATAAGGCTAG TCCGTTATCAACTTGAAAAAGTGGCACCGAGTCG GTGCTTTTTTT) (29)....

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  • ...in bacteria (30,32), yeast (33), zebrafish (34–36), fruit fly (37) and human cells (28,29,38)]....

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Journal ArticleDOI
28 Feb 2013-Cell
TL;DR: This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale and can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects.

4,282 citations


Additional excerpts

  • ...in bacteria (30,32), yeast (33), zebrafish (34–36), fruit fly (37) and human cells (28,29,38)]....

    [...]