CRISPR/CAS9 IN GENOME EDITING: A NATURE GIFTED MOLECULAR TOOL

Authors

  • MA Bashir Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan
  • Q Ali Institute of Biotechnology and Molecular Biology, The University of Lahore, Lahore
  • MS Rashid Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan
  • A Malika Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan

DOI:

https://doi.org/10.54112/bcsrj.v2020i1.18

Keywords:

Cas9/CRISPR, endonucleases, RNA, medical, agriculture, pharamaceutical, livestock

Abstract

The Cas9 protein derived from type II CRISPR as a part of bacterial immune system has been raising up as a useful genetic tool for genomic engineering in various life forms. As RNA-guided DNA endonucleases, the Cas9 could be effectively customized to marked new DNA sequence sites by adjusting guided RNA sequences; it has been appeared as new emerging DNA editing technology. The nuclease-disable types of Cas9 has provided adaptable RNA guided DNA focusing on regulation and visualization of genomic DNA, just as for restoring the epigenetic forms and status, all has been shown in a an accurate sequence. Through these proceed; the researchers have started to explore conceivable uses of Cas9 in medical, agriculture, pharmaceutical and livestock sciences.

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References

Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine, V., Cox, D. B., Kellner, M. J., and Regev, A. (2017). RNA targeting with CRISPR–Cas13. Nature 550, 280-284.

Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., and Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712.

Belotserkovskii, B. P., Tornaletti, S., D’Souza, A. D., and Hanawalt, P. C. (2018). R-loop generation during transcription: Formation, processing and cellular outcomes. DNA repair 71, 69-81.

Bhargava, R., Sandhu, M., Muk, S., Lee, G., Vaidehi, N., and Stark, J. M. (2018). C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains. Nature communications 9, 1-14.

Brouns, S. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J., Snijders, A. P., Dickman, M. J., Makarova, K. S., Koonin, E. V., and Van Der Oost, J. (2008). Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964.

Chen, J. S., and Doudna, J. A. (2017). The chemistry of Cas9 and its CRISPR colleagues. Nature Reviews Chemistry 1, 1-15.

Chen, K., Wang, Y., Zhang, R., Zhang, H., and Gao, C. (2019a). CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual review of plant biology 70, 667-697.

Chen, M., Mao, A., Xu, M., Weng, Q., Mao, J., and Ji, J. (2019b). CRISPR-Cas9 for cancer therapy: Opportunities and challenges. Cancer letters 447, 48-55.

Chen, Y.-C., Sheng, J., Trang, P., and Liu, F. (2018). Potential application of the CRISPR/Cas9 system against herpesvirus infections. Viruses 10, 291.

Chew, W. L. (2018). Immunity to CRISPR Cas9 and Cas12a therapeutics. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 10, e1408.

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., and Marraffini, L. A. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823.

Doxzen, K. W., and Doudna, J. A. (2017). DNA recognition by an RNA-guided bacterial Argonaute. PloS one 12, e0177097.

Dugar, G., Leenay, R. T., Eisenbart, S. K., Bischler, T., Aul, B. U., Beisel, C. L., and Sharma, C. M. (2018). CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Molecular cell 69, 893-905. e7.

Gleditzsch, D., Pausch, P., Müller-Esparza, H., Özcan, A., Guo, X., Bange, G., and Randau, L. (2019). PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA biology 16, 504-517.

Hess, G. T., Tycko, J., Yao, D., and Bassik, M. C. (2017). Methods and applications of CRISPR-mediated base editing in eukaryotic genomes. Molecular cell 68, 26-43.

Hille, F., Richter, H., Wong, S. P., Bratovič, M., Ressel, S., and Charpentier, E. (2018). The biology of CRISPR-Cas: backward and forward. Cell 172, 1239-1259.

Hunter, M. C., Smith, R. G., Schipanski, M. E., Atwood, L. W., and Mortensen, D. A. (2017). Agriculture in 2050: recalibrating targets for sustainable intensification. Bioscience 67, 386-391.

Hwang, S., and Maxwell, K. L. (2019). Meet the anti-CRISPRs: Widespread protein inhibitors of CRISPR-Cas systems. The CRISPR journal 2, 23-30.

Jackson, S. A., McKenzie, R. E., Fagerlund, R. D., Kieper, S. N., Fineran, P. C., and Brouns, S. J. (2017). CRISPR-Cas: Adapting to change. Science 356.

Jiang, F., and Doudna, J. A. (2017). CRISPR–Cas9 structures and mechanisms. Annual review of biophysics 46, 505-529.

Knott, G. J., and Doudna, J. A. (2018). CRISPR-Cas guides the future of genetic engineering. Science 361, 866-869.

Koonin, E. V., and Makarova, K. S. (2019). Origins and evolution of CRISPR-Cas systems. Philosophical Transactions of the Royal Society B 374, 20180087.

Kosicki, M., Rajan, S. S., Lorenzetti, F. C., Wandall, H. H., Narimatsu, Y., Metzakopian, E., and Bennett, E. P. (2017). Dynamics of indel profiles induced by various CRISPR/Cas9 delivery methods. In "Progress in Molecular Biology and Translational Science", Vol. 152, pp. 49-67. Elsevier.

Lee, Y. T., Tan, Y. J., and Oon, C. E. (2018). Molecular targeted therapy: treating cancer with specificity. European journal of pharmacology 834, 188-196.

Levin, A. A. (2019). Treating disease at the RNA level with oligonucleotides. New England Journal of Medicine 380, 57-70.

Li, K., Cai, D., Wang, Z., He, Z., and Chen, S. (2018). Development of an efficient genome editing tool in Bacillus licheniformis using CRISPR-Cas9 nickase. Applied and Environmental Microbiology 84.

Li, R., Liu, C., Zhao, R., Wang, L., Chen, L., Yu, W., Zhang, S., Sheng, J., and Shen, L. (2019). CRISPR/Cas9-Mediated SlNPR1 mutagenesis reduces tomato plant drought tolerance. BMC plant biology 19, 1-13.

Liu, B., Saber, A., and Haisma, H. J. (2019). CRISPR/Cas9: a powerful tool for identification of new targets for cancer treatment. Drug discovery today 24, 955-970.

Lo, A., and Qi, L. (2017). Genetic and epigenetic control of gene expression by CRISPR–Cas systems. F1000Research 6.

Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J., Charpentier, E., Cheng, D., Haft, D. H., and Horvath, P. (2019). Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nature Reviews Microbiology, 1-17.

Meng, X., Hu, X., Liu, Q., Song, X., Gao, C., Li, J., and Wang, K. (2018). Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice. Science China Life Sciences 61, 122-125.

Mollanoori, H., Shahraki, H., Rahmati, Y., and Teimourian, S. (2018). CRISPR/Cas9 and CAR-T cell, collaboration of two revolutionary technologies in cancer immunotherapy, an instruction for successful cancer treatment. Human immunology 79, 876-882.

Palermo, G., Chen, J. S., Ricci, C. G., Rivalta, I., Jinek, M., Batista, V. S., Doudna, J. A., and McCammon, J. A. (2018). Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’,‘regulating’, and ‘locking’the catalytic HNH domain. Quarterly reviews of biophysics 51.

Palermo, G., Miao, Y., Walker, R. C., Jinek, M., and McCammon, J. A. (2017). CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proceedings of the National Academy of Sciences 114, 7260-7265.

Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., and Zhang, F. (2013). Genome engineering using the CRISPR-Cas9 system. Nature protocols 8, 2281-2308.

Ryan, D. E., Taussig, D., Steinfeld, I., Phadnis, S. M., Lunstad, B. D., Singh, M., Vuong, X., Okochi, K. D., McCaffrey, R., and Olesiak, M. (2018). Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs. Nucleic acids research 46, 792-803.

Saglam-Metiner, P., Gulce-Iz, S., and Biray-Avci, C. (2019). Bioengineering-inspired three-dimensional culture systems: Organoids to create tumor microenvironment. Gene 686, 203-212.

Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., and Doench, J. G. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87.

Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V., and Koonin, E. V. (2018). Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proceedings of the National Academy of Sciences 115, E5307-E5316.

Soyars, C. L., Peterson, B. A., Burr, C. A., and Nimchuk, Z. L. (2018). Cutting edge genetics: CRISPR/Cas9 editing of plant genomes. Plant and Cell Physiology 59, 1608-1620.

Stella, S., Alcón, P., and Montoya, G. (2017). Class 2 CRISPR–Cas RNA-guided endonucleases: Swiss Army knives of genome editing. Nature Structural & Molecular Biology 24, 882.

Terns, M. P., and Terns, R. M. (2011). CRISPR-based adaptive immune systems. Current opinion in microbiology 14, 321-327.

Thornton, P. K., Whitbread, A., Baedeker, T., Cairns, J., Claessens, L., Baethgen, W., Bunn, C., Friedmann, M., Giller, K. E., and Herrero, M. (2018). A framework for priority-setting in climate smart agriculture research. Agricultural Systems 167, 161-175.

Wilson, C. J., Fennell, T., Bothmer, A., Maeder, M. L., Reyon, D., Cotta-Ramusino, C., Fernandez, C. A., Marco, E., Barrera, L. A., and Jayaram, H. (2018). Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”. Nature methods 15, 236-237.

Xia, A.-L., He, Q.-F., Wang, J.-C., Zhu, J., Sha, Y.-Q., Sun, B., and Lu, X.-J. (2019). Applications and advances of CRISPR-Cas9 in cancer immunotherapy. Journal of medical genetics 56, 4-9.

Zeng, Y., Cui, Y., Zhang, Y., Zhang, Y., Liang, M., Chen, H., Lan, J., Song, G., and Lou, J. (2018). The initiation, propagation and dynamics of CRISPR-SpyCas9 R-loop complex. Nucleic acids research 46, 350-361.

Zuo, Z., and Liu, J. (2017). Structure and dynamics of Cas9 HNH domain catalytic state. Scientific reports 7, 1-13.

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Published

2020-12-12

How to Cite

Bashir, M., Ali, Q., Rashid, M., & Malika, A. (2020). CRISPR/CAS9 IN GENOME EDITING: A NATURE GIFTED MOLECULAR TOOL. Biological and Clinical Sciences Research Journal, 2020(1). https://doi.org/10.54112/bcsrj.v2020i1.18

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