An overview of gene editing technology (CRISPR) and its applications in animal science research

Document Type : Scientific-Extensional Article

Authors

1 Ph.D. Student of Animal and Poultry Breeding & Genetics, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran

2 M.Sc. Student of Animal Breeding & Genetics, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran

3 Professor of Animal and Poultry Breeding & Genetics, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran

Abstract

Since the discovery of the helical structure of DNA in 1953, researchers were looking for ways to manipulate the genome. The starting point of the genome editing process began in the 70s with the production of recombinant DNA and the development of genetic engineering and then the commercial production of restriction enzymes. Genome editing refers to the process of targeted modification of the genome and also it is one of the most important advances in genetic engineering in the current century. This technology helped scientists to delete and add or change genetic material to improve performance and create targeted genetic changes in humans, animals, and plants in certain regions of the genome. One of the genome editing tools is the CRISPR system, which has been used as a powerful approach for high-efficiency genome editing in various types of organisms and has created a revolution in biological research. The CRISPR system is an acquired immune system in prokaryotes that protects them against bacteriophages and plasmids. This technique can be used to treat and control genetic diseases, improve the quality of food, make vaccines and drugs, and also to correct and improve the performance of growth and reproduction. In 2020, two scientists named Jennifer Doudna and Emmanuelle Charpentier were awarded the Nobel Prize for inventing the CRISPR technique, which shows the importance and many applications of this technology in the field of medicine and agriculture in the future. This study shows the history, importance, and application of the CRISPR system in animal science to make progress in animal and poultry breeding and take into account ethical standards and animal welfare. This study shows the history, importance, and application of the CRISPR system in animal science to make progress in animal and poultry breeding and take into account ethical standards and animal welfare.

Keywords

References

Abudayyeh, O.O., Gootenberg, J.S., Essletzbichler, P., Han, S., Joung, J and et al. (2017). “RNA targeting with CRISPR-Cas13.” Nature, 12, 550(7675), 280-284.
Abudayyeh, O.O., Gootenberg, J.S., Konermann, S., Joung, J., Slaymaker, I.M., and et al. (2016). “C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.” Science, 353(6299), 5573.‏
Al-Attar, S., Westra, E.R., Van Der Oost, J., and Brouns, S.J. (2011). “Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.‏”
Albitar, A., Rohani, B., Will, B., Yan, A., and Gallicano, G. I. (2018). “The application of CRISPR/Cas technology to efficiently model complex cancer genomes in stem cells.” Journal of Cellular Biochemistry, 119(1), 134-140.‏
Alkhnbashi, O. S., Shah, S. A., Garrett, R. A., Saunders, S. J., Costa, F., and et al. (2016). “Characterizing leader sequences of CRISPR loci.” Bioinformatics, 32(17), i576-i585.‏
Asaduzzaman, M., Juliana, F. M., Ali, M. H., Parvin, M. J., Hossain, S. I., and et al. (2021). “dnaK GENE EDITING IN THE Escherichia coli GENOME VIA THE CAS9/CRISPR SYSTEM.”‏
Aschenbrenner, S., Kallenberger, S. M., Hoffmann, M. D., Huck, A., Eils, R., and et al. (2020). “Coupling Cas9 to artificial inhibitory domains enhances CRISPR-Cas9 target specificity.” Science Advances, 6(6), eaay0187.
Barman, A., Deb, B., and Chakraborty, S. (2020). “A glance at genome editing with CRISPR–Cas9 technology.” Current Genetics, 66(3), 447-462.‏
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., and et al. (2007). “CRISPR provides acquired resistance against viruses in prokaryotes.” Science, 315(5819), 1709-1712.‏
Behr, M., Zhou, J., Xu, B., and Zhang, H. (2021). “In vivo delivery of CRISPR-Cas9 therapeutics: Progress and challenges.” Acta Pharmaceutica Sinica B, 11(8), 2150-2171.‏
Bondy-Denomy, J., Garcia, B., Strum, S., Du, M., Rollins, M. F., and et al. (2015). “Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins.” Nature, 526(7571), 136-139.‏‏
Chen, G., Wei, T., Yang, H., Li, G., and Li, H. (2022). “CRISPR-Based Therapeutic Gene Editing for Duchenne Muscular Dystrophy: Advances, Challenges and Perspectives.” Cells, 11(19), 2964.‏
Chen, J. S., Dagdas, Y. S., Kleinstiver, B. P., Welch, M. M., Sousa, A. A., and et al. (2017). “Enhanced proofreading governs CRISPR–Cas9 targeting accuracy.” Nature, 550(7676), 407-410.‏
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., and et al. (2013). “Multiplex genome engineering using CRISPR/Cas systems.” Science, 339(6121), 819-823.‏
Crudele, J. M., and Chamberlain, J. S. (2018). “Cas9 immunity creates challenges for CRISPR gene editing therapies.” Nature Communications, 9(1), 1-3.‏
Davis, A. J., and Chen, D. J. (2013). “DNA double strand break repair via non-homologous end-joining.” Translational Cancer Research, 2(3), 130.‏
Doench, J. G. (2018). “Am I ready for CRISPR? A user's guide to genetic screens.” Nature Reviews Genetics, 19(2), 67-80.‏
Dong, O. X., Yu, S., Jain, R., Zhang, N., Duong, P. Q., and et al. (2020). “Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9.” Nature Communications, 11(1), 1-10.‏
Doudna Jennifer, A., and Charpentier, E. (2014). “The new frontier of genome engineering with CRISPR-Cas9.” Science, 346(6213), 1258096.‏
Fonfara, I., Richter, H., Bratovič, M., Le Rhun, A., and Charpentier, E. (2016). “The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA.” Nature, 532(7600), 517-521.‏
Friedland, A. E., Baral, R., Singhal, P., Loveluck, K., Shen, S., and et al. (2015). “Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications.” Genome Biology, 16(1), 1-10.‏
Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., and Joung, J. K. (2014). “Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.” Nature Biotechnology, 32(3), 279-284.‏
Gao, Y., Wu, H., Wang, Y., Liu, X., Chen, L., and et al. (2017). “Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects.” Genome Biology, 18(1), 1-15.‏
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., and et al. (2013). “CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.” Cell, 154(2), 442-451.‏
Guilinger, J. P., Thompson, D. B., and Liu, D. R. (2014). “Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification.” Nature Biotechnology, 32(6), 577-582.‏
Hille, F., and Charpentier, E. (2016). “CRISPR-Cas: biology, mechanisms and relevance.” Philosophical transactions of the royal society B: biological Sciences, 371(1707), 20150496.‏
Hu, R., Fan, Z.Y., Wang, B.Y., Deng, S.L., Zhang, X.S., and et al. (2017) “Generation of FGF5 knockout sheep via the CRISPR/Cas9 system.” Journal of Animal Science, 95(5), 2019-2024.
Hu, J. H., Miller, S. M., Geurts, M. H., Tang, W., Chen, L., and et al. (2018). “Evolved Cas9 variants with broad PAM compatibility and high DNA specificity.” Nature, 556(7699), 57-63.‏
Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., and Nakata, A. (1987). “Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product.” Journal of Bacteriology, 169(12), 5429-5433.‏
Jiang, F., and Doudna, J. A. (2017). “CRISPR-Cas9 structures and mechanisms.” Annu Rev Biophys, 46(1), 505-529.‏
Jiang, F., Zhou, K., Ma, L., Gressel, S., and Doudna, J. A. (2015). “A Cas9–guide RNA complex preorganized for target DNA recognition.” Science, 348(6242), 1477-1481.‏
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and et al. (2012). “A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity.” Science, 337(6096), 816-821.‏
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., and et al. (2014). “Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.” Science, 343(6176), 1247997.‏
Kalds, P., Crispo, M., Li, C., Tesson, L., Anegón, I., and et al. (2022). “Generation of Double-Muscled Sheep and Goats by CRISPR /Cas9-Mediated Knockout of the Myostatin Gene.” Methods in Molecular Biology, 2495, 295-323.
Khalil, A. M. (2020). “The genome editing revolution.” Journal of Genetic Engineering and Biotechnology, 18(1), 1-16.‏
Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., and et al. (2016). “High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects.” Nature, 529(7587), 490-495.‏
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., and et al. (2015). “Engineered CRISPR-Cas9 nucleases with altered PAM specificities.” Nature, 523(7561), 481-485
Koonin, E. V., and Makarova, K. S. (2019). “Origins and evolution of CRISPR-Cas systems.” Philosophical Transactions of the Royal Society B, 374(1772), 20180087.‏
Koonin, E. V., Makarova, K. S., and Zhang, F. (2017). “Diversity, classification and evolution of CRISPR-Cas systems.” Current Opinion in Microbiology, 37, 67-78.‏
Lattanzi, A., Meneghini, V., Pavani, G., Amor, F., Ramadier, S., and et al. (2019). “Optimization of CRISPR/Cas9 delivery to human hematopoietic stem and progenitor cells for therapeutic genomic rearrangements.” Molecular Therapy, 27(1), 137-150.‏
Lee, J., Kim, D. H., and Lee, K. (2020). “Muscle hyperplasia in Japanese quail by single amino acid deletion in MSTN propeptide.” International Journal of Molecular Sciences, 21(4), 1504.‏
Lee, K., Conboy, M., Park, H. M., Jiang, F., Kim, H. J., and et al. (2017). “Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair.” Nature Biomedical Engineering, 1(11), 889-901.‏
Ma, T., Tao, J., Yang, M., He, C., Tian, X., and et al. (2017). “An AANAT/ASMT transgenic animal model constructed with CRISPR/Cas9 system serving as the mammary gland bioreactor to produce melatonin‐enriched milk in sheep.” Journal of Pineal Research, 63(1), e12406.‏
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., and Koonin, E. V. (2006). “A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.” Biology Direct, 1(1), 1-26.‏
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., and et al. (2020). “Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants.” Nature Reviews Microbiology, 18(2), 67-83.‏
Marraffini, L. A. (2015). “CRISPR-Cas immunity in prokaryotes.” Nature, 526(7571), 55-61.‏
Menchaca, A., Dos Santos-Neto, P.C., Mulet, A.P., and Crispo, M. (2020). “CRISPR in livestock: From editing to printing.” Theriogenology, 150, 247-254. 
Naldini, L., Trono, D., and Verma, I. M. (2016). “Lentiviral vectors, two decades later.” Science, 353(6304), 1101-1102.‏
Pannunzio, N. R., Watanabe, G., and Lieber, M. R. (2018). “Nonhomologous DNA end-joining for repair of DNA double-strand breaks.” Journal of Biological Chemistry, 293(27), 10512-10523.‏
Paul, B., and Montoya, G. (2020). “CRISPR-Cas12a: Functional overview and applications.” Biomedical Journal, 43(1), 8-17.‏
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., and et al. (2013). “Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.” Cell, 152(5), 1173-1183.‏
Ran, F. A. C. L., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., and et al. (2015). “In vivo genome editing using Staphylococcus aureus Cas9.” Nature, 520(7546), 186-191.‏
Ran, F. A. F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., and et al. (2013). “Genome engineering using the CRISPR-Cas9 system.” Nature Protocols, 8(11), 2281-2308.‏
Ryczek, N., Hryhorowicz, M., Zeyland, J., Lipiński, D., and Słomski, R. (2021). “CRISPR/Cas technology in pig-to-human xenotransplantation research.” International Journal of Molecular Sciences, 22(6), 3196.‏
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., and et al. (2015). “Discovery and functional characterization of diverse class 2 CRISPR-Cas systems.” Molecular Cell, 60(3), 385-397.
Slaymaker, I. M., Gao, L., Zetsche, B., Scott, D. A., Yan, W. X., and et al. (2016). “Rationally engineered Cas9 nucleases with improved specificity.” Science, 351(6268), 84-88.‏
Tait-Burkard, C., Doeschl-Wilson, A., McGrew, M.J., Archibald, A.L., Sang, H.M., and et al. (2018). “Livestock 2.0 – genome editing for fitter, healthier, and more productive farmed animals.” Genome Biology, 19, 204.
Tsai, S. Q., Wyvekens, N., Khayter, C., Foden, J. A., Thapar, V., and et al. (2014). “Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.” Nature Biotechnology, 32(6), 569-576.‏
Vilarino, M., Rashid, S. T., Suchy, F. P., McNabb, B. R., Van Der Meulen, T., and et al. (2017). “CRISPR/Cas9 microinjection in oocytes disables pancreas development in sheep.” Scientific Reports, 7(1), 1-10.‏
Wang, D., Tai, P. W., and Gao, G. (2019). “Adeno-associated virus vector as a platform for gene therapy delivery.” Nature Reviews Drug Discovery, 18(5), 358-378.‏
Wang, M., Zuris, J. A., Meng, F., Rees, H., Sun, S., and et al. (2016). “Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles.” Proceedings of the National Academy of Sciences, 113(11), 2868-2873.‏
Yang, G., and Huang, X. (2019). “Methods and applications of CRISPR/Cas system for genome editing in stem cells.” Cell Regeneration, 8(2), 33-41.‏
Yao, R., Liu, D., Jia, X., Zheng, Y., Liu, W., and et al. (2018). “CRISPR-Cas9/Cas12a biotechnology and application in bacteria.” Synthetic and Systems Biotechnology, 3(3), 135-149.‏
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., and et al. (2015). “Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.” Cell, 163(3), 759-771.‏
Zhang, Z., Zhang, Y., Gao, F., Han, S., Cheah, K. S., and et al. (2017). “CRISPR/Cas9 genome-editing system in human stem cells: current status and future prospects.” Molecular Therapy-Nucleic Acids, 9, 230-241.‏
Zhao, Z., Li, C., Tong, F., Deng, J., Huang, G., and et al. (2021). “Review of applications of CRISPR-Cas9 gene-editing technology in cancer research.” Biological Procedures Online, 23(1), 1-13.‏
Zou, Z., Huang, K., Wei, Y., Chen, H., Liu, Z., and et al. (2017). “Construction of a highly efficient CRISPR/Cas9-mediated duck enteritis virus-based vaccine against H5N1 avian influenza virus and duck Tembusu virus infection.” Scientific Reports, 7(1), 1-12.‏

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