scholarly journals CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments

Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1033 ◽  
Author(s):  
Jake Adolf V. Montecillo ◽  
Luan Luong Chu ◽  
Hanhong Bae

Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 56-56
Author(s):  
Michael Thomson

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.


Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 797
Author(s):  
Muntazir Mushtaq ◽  
Aejaz Ahmad Dar ◽  
Milan Skalicky ◽  
Anshika Tyagi ◽  
Nancy Bhagat ◽  
...  

Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.


Author(s):  
T Tahir ◽  
Q Ali ◽  
MS Rashid ◽  
A Malik

Today we can use multiple of endonucleases for genome editing which has become very important and used in number of applications. We use sequence specific molecular scissors out of which, most important are mega nucleases, zinc finger nucleases, TALENS (Transcription Activator Like-Effector Nucleases) and CRISPR-Cas9 which is currently the most famous due to a number of reasons, they are cheap, easy to build, very specific in nature and their success rate in plants and animals is also high. Who knew that one day these CRISPR discovered as a part of immune system of bacteria will be this much worthwhile in the field of genetic engineering? This review interprets the science behind their mechanism and how several advancements were made with the passage of time to make them more efficient for the assigned job.


2020 ◽  
Author(s):  
Yang Zhang ◽  
Jifeng Yuan

ABSTRACTPurple non-sulfur photosynthetic bacteria (PNSB) such as R. capsulatus serve as a versatile platform for fundamental studies and various biotechnological applications. In this study, we sought to develop the class II RNA-guided CRISPR/Cas12a system from Francisella novicida for both genome editing and gene down-regulation in R. capsulatus. About 90% editing efficiency was achieved by using CRISPR/Cas12a driven by a strong promoter Ppuc when targeting ccoO or nifH gene. When both genes were simultaneously targeted, the multiplex gene editing efficiency reached >63%. In addition, CRISPR interference using deactivated Cas12a was also evaluated using reporter genes gfp and lacZ, and the repression efficiency reached >80%. In summary, our work represents the first report to develop CRISPR/Cas12a mediated genome editing/transcriptional repression in R. capsulatus, which would greatly accelerate PNSB-related researches.IMPORTANCEPurple non-sulfur photosynthetic bacteria (PNSB) such as R. capsulatus serve as a versatile platform for fundamental studies and various biotechnological applications. However, lack of efficient gene editing tools remains a main obstacle for progressing in PNSB-related researches. Here, we developed CRISPR/Cas12a for genome editing via the non-homologous end joining (NHEJ) repair machinery in R. capsulatus. In addition, DNase-deactivated Cas12a was found to simultaneously suppress multiple targeted genes. Taken together, our work offers a new set of tools for efficient genome engineering in PNSB such as R. capsulatus.


2021 ◽  
Author(s):  
Joao M. Fernandes Neto ◽  
Katarzyna Jastrzebski ◽  
Cor Lieftink ◽  
Lenno Krenning ◽  
Matheus Dias ◽  
...  

CRISPR technology is an invaluable tool for large-scale functional genomic screening. Genome editing efficiency and timing are important parameters impacting the performance of pooled CRISPR screens. Here we show that by optimizing Cas9 expression levels, the time necessary for gene editing can be reduced contributing to improved performance of CRISPR based screening.


2021 ◽  
Author(s):  
Kaiqun Dai ◽  
Hongxin Fu ◽  
Xiaolong Guo ◽  
Chunyun Qu ◽  
Jufang Wang

Abstract Background: Thermophilic microbes for biofuels and chemicals have attracted great attention due to their tolerance of high temperature and wide range of substrate utilization. Thermoanaerobacterium aotearoense SCUT27 has the ability of glucose and xylose co-utilization in lignocellulosic biomass. Polygene manipulation was a bottleneck since it was hindered by available markers for selection. In this study, the endogenous Type I-B CRISPR/Cas system was developed for multiplex genome editing in SCUT27. Results: The protospacer-adjacent motif (PAM) was identified by in silico and orotidine-5’-phosphate decarboxylase (pyrF) and then lactate dehydrogenase (ldh) were chosen as the editing target to assess the toxicity of this immune system and gene editing efficiency. The mutants could be repeatedly obtained with an editing efficiency of 58.3-100%. Higher transformation efficiency was observed after optimization of some editing strategies. Furthermore, a new method was performed for screening mutants of plasmid curing (recycling of the editing plasmid) for multiplex genome editing based on the negative selection marker tdk, and then ldh and arginine repressor (argR) were knocked out successively. The mutant SCUT27/Δldh/ΔargR had the prominent advantages over SCUT27 for ethanol production with enhanced ability to metabolize xylose. When cultured under various lignocellulosic hydrolysates, the mutant showed a satisfactory performance with the ethanol titer and yield improved by 147.42–739.40% and 112.67–267.89%, respectively, compared with SCUT27, as well as the enhanced tolerance to inhibitors.Conclusion: The multi-gene editing by native CRISPR/Cas system is a promising strategy to engineer SCUT27 for higher ethanol production with lignocellulosic hydrolysates.


2016 ◽  
Vol 41 (3) ◽  
pp. 1-3
Author(s):  
Nicanor Pier Giorgio Austriaco ◽  

There has been much discussion regarding the proper use of the powerful CRISPR technologies that can be used to edit the genome. CRISPR is a technique borrowed from bacterial cells that will allow scientists to quickly and precisely change the DNA of nearly any organism, including humans. Unlike other gene-editing technologies, CRISPR is cheap, quick, and easy to use. In fact, do-it-yourself CRISPR genome editing kits are available online for less than $200, which will enable anyone, including so-called biohackers, to do genetic engineering at the kitchen table. In only three years—CRISPR as a genome-editing tool was first described in 2012—it is already universally acknowledged that this technology will revolutionize the life sciences. But CRISPR’s great promise has also sparked a great ethical and societal debate on its legitimate uses, most significantly on whether it should be used to alter the genomes of our children and grandchildren.


2020 ◽  
Vol 3 (1) ◽  
pp. 31-39
Author(s):  
Y. V. Kuzmina

Genome editing methods are now widely used in research aimed at studying fundamental biological processes, in particular for regulating maturation and extending shelf life of plant agricultural products. This review briefly discusses plant genome editing methods and examples of their successful application for increasing the storage life of fruits of tomato as one of the most important crops. Genome editing is one of the new areas of genetic engineering that is truly revolutionary in biotechnology. Various genome editing systems have been developed over the past decades: zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and clustered regularly located short palindromic repeats recognized by Cas9 nuclease (CRISPR/Cas9). The most common and widely used is the CRISPR/ Cas9 system, which has many advantages over other existing genome editing systems.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2037-2037
Author(s):  
Takenobu Nii ◽  
Hiroshi Kohara ◽  
Tomotoshi Marumoto ◽  
Tetsushi Sakuma ◽  
Takashi Yamamoto ◽  
...  

Abstract Human pluripotent stem cells (hPSCs), such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), have the potential to self-renew indefinitely and differentiate into various cell types. hPSCs can differentiate into various stem or progenitor cell populations used for regenerative medicine and drug development. Newly developed genome editing technology has advanced the use of hPSCs for such purposes. However, to fully utilize hPSCs to achieve this goal, more efficient gene transfer methods under defined conditions are required. Development of efficient genome editing methods, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9), for use in hPSCs holds great promise in the fields of basic and clinical research. Among these methods, TALENs are more efficient and safer for use in hPSCs to achieve specific gene editing, as ZFNs had a low gene editing efficiency and CRISPR/Cas9 was accompanied by more severe off-target effects than TALENs. Electroporation is a widely used transfection method for hPSC genome editing; however, this method results in reduced cell viability and gene editing efficiency. In the past decade, various methods were developed for gene transfer into hPSCs; however, hPSCs form tightly packed colonies, making gene transfer difficult. In this study, we established a culture method of hPSCs at a single-cell-state to reduce cell density, and investigated gene transfection efficiency followed by gene editing efficiency. hPSCs cultured in a single-cell-state were transfected using non-liposomal transfection reagents with plasmid DNA driven by the human elongation factor 1-alpha 1 (EF1α) promoter or mRNA encoding enhanced green fluorescent protein (eGFP). The proportion of eGFP+ cells considerably increased in single-cell-state cultures (DNA: 95.80 ± 2.51%, mRNA: 99.70 ± 0.10%). Moreover, most of the cells were viable (control: 93.10 ± 0.40%, DNA: 83.40 ± 2.03%, mRNA: 86.71 ± 0.19%). The mean fluorescence intensity (MFI) was approximately three-fold higher than that in cells transfected by electroporation (electroporation (EPN): 6631 ± 992; transfection (TFN): 17933 ± 1595). eGFP expression was detected by fluorescence microscopy until day seven post-transfection. Our results also demonstrate an inverse correlation between cell density and transfection efficiency. To test whether transfection using this method affected the "stemness" of hPSCs, we examined SSEA4 and NANOG expression in eGFP-transfected cells by flow cytometry analysis. The percentage of both SSEA4+ and NANOG+ cells was greater than 90%. Moreover, transplantation of eGFP-transfected cells into immunodeficient mice led to the formation of teratomas. These results strongly suggested that single-cell-state hPSC culture improved transfection efficiency without inducing differentiation or loss of pluripotency. Moreover, we used our efficient transfection method to edit the hPSC genome using TALENs. We constructed a Platinum TALEN driven by the EF1α promoter targeting the adenomatous polyposis coli (APC) gene and analyzed the efficiency of gene editing using the Cel-1 assay. Our efficient transfection method induced mutations more efficiently than electroporation (Transfection: 11.1 ± 1.38%, Electroporation: 3.2 ± 0.89). These results showed that TALENs increased gene editing efficiency in single-cell-state hPSC cultures. Overall, our efficient hPSC transfection method using single-cell-state culture provides an excellent experimental system to investigate the full potential of hPSCs. We expect that this method may contribute to the fields of hPSC-based regenerative medicine and drug discovery. Disclosures No relevant conflicts of interest to declare.


Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3156
Author(s):  
Shivohum Bahuguna ◽  
Siamak Redhai ◽  
Jun Zhou ◽  
Tianyu Wang ◽  
Fillip Port ◽  
...  

CRISPR-Cas has revolutionized genetics and extensive efforts have been made to enhance its editing efficiency by developing increasingly more elaborate tools. Here, we evaluate the CRISPR-Cas9 system in Drosophila melanogaster to assess its ability to induce stem cell-derived tumors in the intestine. We generated conditional tissue-specific CRISPR knockouts using different Cas9 expression vectors with guide RNAs targeting the BMP, Notch, and JNK pathways in intestinal progenitors such as stem cells (ISCs) and enteroblasts (EBs). Perturbing Notch and BMP signaling increased the proliferation of ISCs/EBs and resulted in the formation of intestinal tumors, albeit with different efficiencies. By assessing both the anterior and posterior regions of the midgut, we observed regional differences in ISC/EB proliferation and tumor formation upon mutagenesis. Surprisingly, high continuous expression of Cas9 in ISCs/EBs blocked age-dependent increase in ISCs/EBs proliferation and when combined with gRNAs targeting tumor suppressors, it prevented tumorigenesis. However, no such effects were seen when temporal parameters of Cas9 were adjusted to regulate its expression levels or with a genetically modified version, which expresses Cas9 at lower levels, suggesting that fine-tuning Cas9 expression is essential to avoid deleterious effects. Our findings suggest that modifications to Cas9 expression results in differences in editing efficiency and careful considerations are required when choosing reagents for CRISPR-Cas9 mutagenesis studies. In summary, Drosophila can serve as a powerful model for context-dependent CRISPR-Cas based perturbations and to test genome-editing systems in vivo.


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