ADVANCES IN RESEARCH ON GENOME EDITING CRISPR-CAS9 TECHNOLOGY

Authors

  • Syed Zawar Shah Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
  • Anum Rehman Center of Biotechnology and Microbiology, University of Peshawar, Pakistan
  • Hira Nasir Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
  • Azka Asif School of Biological Sciences, University of Punjab, Lahore, Pakistan
  • Bakhtawar Tufail Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
  • Muhammad Usama Ayub Medical College, Abbottabad, Pakistan
  • Basit Jabbar Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan

Abstract

The current era of genome engineering has been revolutionized by the evolution of a bacterial adaptive immune system, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) into a radical technology that is making an expeditious progress in its mechanism, function and applicability. Utilizing a non-specific Cas9 nuclease and a sequence specific programmable CRISPR RNA (crRNA), this system cleaves the target DNA with high precision. With a vast potential for profound implications, CRISPR has emerged as a mainstream method for plausible genomic manipulations in a range of organisms owing to its simplicity, accuracy and speed. A modified form of CRISPR system, known as CRISPR/Cpf1 that employs a smaller and simpler endonuclease (Cpf1) than Cas9, can be used to overcome certain limitations of CRISPR/Cas9 system. Despite clear-cut innovative biological applications, this technology is challenged by off-target effects and associated risks, so safe and controlled implementation is needed to enable this emerging technique assist both biological research and translational applications. In this review, we intend to elucidate different aspects of CRISPR in the light of current advancements.

Author Biographies

Syed Zawar Shah, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan

Research Associate at Biopharmaceutical Lab, CEMB, PU

Anum Rehman, Center of Biotechnology and Microbiology, University of Peshawar, Pakistan

MPhil Scholar

Hira Nasir, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan

Research Associate

Azka Asif, School of Biological Sciences, University of Punjab, Lahore, Pakistan

MPhil Scholar

Bakhtawar Tufail, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan

MPhil Scholar

Muhammad Usama, Ayub Medical College, Abbottabad, Pakistan

MBBS

References

Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010;11(3):181–90.

Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes. Science 2008;321(5891):960–4.

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012;337(6096):816–21.

Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods 2013;10(10):957–63.

Makarova KS, Aravind L, Wolf YI, Koonin EV. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 2011;6(1):38.

Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013;31(3):233–9.

Zhang F, Wen Y, Guo X. CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet 2014;23(R1):R40–6.

Hsu PD, Lander ES, Zhang F. Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 2014;157(6):1262–78.

Broad Institute prevails in heated dispute over CRISPR patents [Internet]. STAT. 2017 [cited 2017 Mar 2]. Available from: https://www.statnews.com/2017/02/15/crispr-patent-ruling/

European Patent Office to grant UC a broad patent on CRISPR-Cas9. Berkeley News. [Internet]. [cited 2017 Mar 30]. Available from: http://news.berkeley.edu/2017/03/28/european-patent-office-to-grant-uc-a-broad-patent-on-crispr-cas9/

Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science 2007;315(5819):1709–12.

Van der Oost J, Westra E, Jackson RN, Wiedenheft B. Unravelling the structural and mechanistic basis of CRISPR–Cas systems. Nat Rev Microbiol 2014;12(7):479–92.

Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013;31(9):827–32.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013;339(6121):819–23.

Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 2012;109(39):E2579–86.

Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014;156:935–49.

Davis L, Maizels N. Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc Natl Acad Sci 2014;111(10):E924–32.

Sander JD, Joung JK. CRISPR–Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014;32(4):347–55.

Mladenov E, Iliakis G. Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways. Mutat Res 2011;711(1-2):61–72.

Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR–Cas9. Science 2014;346(6213):1258096.

Jinek M, Jiang F, Taylor D, Sternberg S, Kaya E, Ma E. et al. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation. Science 2014;343(6176):1247997.

Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 2014;513(7519):569–73.

Szczelkun M, Tikhomirova M, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci U S A 2014;111(27):9798–803.

Ledford H. Alternative CRISPR system could improve genome editing. Nature 2015;526(7571):17.

Lin Y, Cradick T, Brown M, Deshmukh H, Ranjan P, Sarode N, et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 2014;42(11):7473–85.

Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 2015;520(7546):186–91.

Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, et al. Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 2013;31(9):833–8.

Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 2014;32(3):279–84.

Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 2013;31(9):839–43.

Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014;32(6):569–76.

Mei Y, Wang Y, Chen H, Sun ZS, Ju XD. Recent progress in CRISPR/Cas9 technology. J Genet Genomics 2016;43(2):63–75.

Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 2013;493(7432):429–32.

Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson A. A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa. Mbio 2014;5(2):e00896.

Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalog-Reyes Y, et al. Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins. Nature 2015;526(7571):136–9.

Wang J, Ma J, Cheng Z, Meng X, You L, Wang M, Zhang X, et al. A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses. Cell Res 2016;26(10):1165–8.

Deveau H, Barrangou R, Garneau JE, Labonte J, Fremaux C, Boyaval P, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 2008;190(4):1390–1400.

Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 2011;39(21):9275–82.

Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A 2011;108(25):10098–103.

Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun 2012;3:945.

Richter C, Chang JT, Fineran PC. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR Associated (Cas) systems. Viruses 2012;4(10):2291–311.

Beets R. Governing CRISPR: Evaluating Ethics, Risk, and Regulation in Gene Drive Research 2016. [Internet]. [cited 2017 Mar 17]. Available from: http://www.beccabeets.com/wp-content/uploads/Rebecca-Beets-Plan-B-Final.pdf

Pellagatti A, Dolatshad H, Valletta S, Boultwood J. Application of CRISPR/Cas9 genome editing to the study and treatment of disease. Arch Toxicol 2015;89(7):1023–34.

Seruggia D, Montoliu L. The new CRISPR–Cas system: RNA-guided genome engineering to efficiently produce any desired genetic alteration in animals. Transgenic Res 2014;23(5):707–16.

Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 2013;31(8):691–3.

Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 2013;31(8):686–8.

Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, et al. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 2014;12(6):797–807.

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 2014;32(9):947–51.

Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 2013;41(20):e188.

Ali Z, Abul-faraj A, Li L, Ghosh N, Piatek M, Mahjoub A, et al. Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Mol Plant 2015;8(8):1288–91.

Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz MM. CRISPR/Cas9 mediated viral interference in plants. Genome Biol 2015;16(1):238.

Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M. et al. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol 2016;17(7):1140–53.

Borel B. CRISPR, microbes and more are joining the war against crop killers. Nature 2017;543(7645):302–4.

Samanta MK, Dey A, Gayen S. CRISPR/Cas9: an advanced tool for editing plant genomes. Transgenic Res 2016;25(5):561–73.

Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci U S A 2014;111(12):4632–7.

Xie K, Yang Y. RNA-guided genome editing in plants using a CRISPR–Cas system. Mol Plant 2013;6(6):1975–83.

Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res 2014;42(17):10903–14.

Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol 2014;166(2):455–69.

Brooks C, Nekrasov V, Lippman ZB, Van Eck J. Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol 2014;166(3):1292–7.

Gao Y, Zhao Y. Specific and heritable gene editing in Arabidopsis. Proc Natl Acad Sci U S A 2014;111(12):4357–8.

Ueta R, Abe C, Watanabe T, Sugano SS, Ishihara R, Ezura H, et al. Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9. Sci Rep 2017;7(1):507.

Jacobs TB, LaFayette RJ, Schmitz RJ, Parrott WA. Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 2015;15(1):16.

Goodin MM, Zaitlin D, Naidu RA, Lommel SA. Nicotiana benthamiana: its history and future as a model for plant–pathogen interactions. Mol Plant Microbe Interact 2008;21(8):1015–26.

Voytas DF. Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 2013;64:327–50.

Sugano SS, Shirakawa M, Takagi J, Matsuda T, Shimada T, Hara-Nishimura I, et al. CRISPR/Cas9 mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol 2014;55(3):475–81.

Jiang W, Yang B, Weeks DP. Efficient CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS One 2014;9(6):e99225.

Heintze J, Luft C, Ketteler R. A CRISPR CASe for high-throughput silencing. Front Genet 2013;4:193.

Bortesi L, Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 2015;33(1):41–52.

Ramalingam S, Annaluru N, Chandrasegaran S. A CRISPR way to engineer the human genome. Genome Biol 2013;14(2):107.

Barrangou R, Birmingham A, Wiemann S, Beijersbergen RL, Hornung V, Smith Av. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res 2015;43(7):3407–19.

Cox DB, Platt RJ, Zhang F. Therapeutic genome editing: prospects and challenges. Nat Med 2015;21(2):121–31.

LaFountaine JS, Fathe K, Smyth HD. Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9. Int J Pharm 2015;494(1):180–94.

Xiao-Jie L, Hui-Ying X, Zun-Ping K, Jin-Lian C, Li-Juan J. CRISPR-Cas9: a new and promising player in gene therapy. J Med Genet 2015;52(5):289–96.

Araki M, Ishii T. Providing appropriate risk information on genome editing for patients. Trends Biotechnol 2016;34(2):86–90.

Yoon J. The Imperative Need to Consider the Bioethics of CRISPR-Cas9 Technology. NHSJS. [Internet]. 2016. [cited 2017 Mar 30]. Available from: http://nhsjs.com/2016/the-imperative-need-to-consider-the-bioethics-of-crispr-cas9-technology/

Published

2018-12-09

Issue

Vol. 31 No. 1 (2019): JOURNAL OF AYUB MEDICAL COLLEGE, ABBOTTABAD

Section

REVIEW ARTICLE

License

Journal of Ayub Medical College, Abbottabad is an OPEN ACCESS JOURNAL which means that all content is FREELY available without charge to all users whether registered with the journal or not. The work published by J Ayub Med Coll Abbottabad is licensed and distributed under the creative commons License  CC BY ND Attribution-NoDerivs. Material printed in this journal is OPEN to access, and are FREE for use in academic and research work with proper citation. J Ayub Med Coll Abbottabad accepts only original material for publication with the understanding that except for abstracts, no part of the data has been published or will be submitted for publication elsewhere before appearing in J Ayub Med Coll Abbottabad. The Editorial Board of J Ayub Med Coll Abbottabad makes every effort to ensure the accuracy and authenticity of material printed in J Ayub Med Coll Abbottabad. However, conclusions and statements expressed are views of the authors and do not reflect the opinion/policy of J Ayub Med Coll Abbottabad or the Editorial Board.

USERS are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author. This is in accordance with the BOAI definition of open access.

AUTHORS retain the rights of free downloading/unlimited e-print of full text and sharing/disseminating the article without any restriction, by any means including twitter, scholarly collaboration networks such as ResearchGate, Academia.eu, and social media sites such as Twitter, LinkedIn, Google Scholar and any other professional or academic networking site.