Open Access Open Access  Restricted Access Subscription or Fee Access

New Frontiers in Genome Editing: A Comparative of I and II Generation Genome Editing Tools

Dolly Sharma, Bhaswati Banerjee

Abstract


ABSTRACT

Genome editing with programmable site-specific nucleases is an emerging technology. Preliminary applications of I and II generation genome editing tools. It enables the manipulation of targeted genes in many organisms. There are three fundamental technologies are Zinc Finger nuclease (ZFNs), Transcription activator like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (TALENs)-CRISPR-associated protein 9 (Cas-9). This review focus on the significant applications and advantages CRISPR/Cas9 system and concludes with highlighting the limitations and scope of improvements.

 

Keywords: Genome editing tools, CRISPR, zinc finger nuclease, transcription activator, applications

Cite this Article: Dolly Sharma, Bhaswati Banerjee. New Frontiers in Genome Editing: A Comparative of I and II Generation Genome Editing Tools. International Journal of Genetic Engineering and Recombination. 2020; 6(2): 48–65p.


Full Text:

PDF

References


Pabo CO, Peisach E, Grant RA. Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem. 2001;70:313–40. doi: 10.1146/annurev.biochem.70.1.313, PMID 11395410.

Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science. 2009;326(5959):1501. doi: 10.1126/science.1178817, PMID 19933106. Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S2013.

van der Oost J. Molecular biology. New tool for genome surgery. Science. 2013;339(6121):768–70. doi: 10.1126/science.1234726, PMID 23413345. Plant genome engineering with sequence-specific nucleases.

Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science. 2009;326(5959):1501. doi: 10.1126/science.1178817, PMID 19933106.

Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009;326(5959):1509–12. doi: 10.1126/science.1178811, PMID 19933107.

Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186(2):757–61. doi: 10.1534/genetics.110.120717, PMID 20660643.

Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I. FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci U S A. 1998;95(18):10570–5. doi: 10.1073/pnas.95.18.10570, PMID 9724744.

Mukherjee S, Thrasher AJ. Gene therapy for PIDs: progress, pitfalls and prospects. Gene. 2013;525(2):174–81. doi: 10.1016/j.gene.2013.03.098, PMID 23566838.

Grau J, Boch J, Posch S. TALEN offer: genome-wide TALEN off-target prediction. Bioinformatics. 2013;29(22):2931–2. doi: 10.1093/bioinformatics/btt501, PMID 23995255.

Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ. Targeted genome editing across species using ZFNs and TALENs. Science. 2011;333(6040):307. doi: 10.1126/science.1207773, PMID 21700836.

Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol. 2011;29(2):143–8. doi: 10.1038/nbt.1755, PMID 21179091.

Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186(2):757–61. doi: 10.1534/genetics.110.120717, PMID 20660643.

Gaj T, Gersbach CA, Barbas CF 3rd. ZFN, TALEN, and CRISPR/Cas based methods for genome engineering. Trends Biotechnol. 2013;31(7):397–405. doi: 10.1016/j.tibtech.2013.04.004, PMID 23664777.

Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24(1):132–41. doi: 10.1101/gr.162339.113, PMID 24253446.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23. doi: 10.1126/science.1231143, PMID 23287718.

Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823–6. doi: 10.1126/science.1232033, PMID 23287722.

Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013;31(9):833–8. doi: 10.1038/nbt.2675, PMID 23907171.

Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827–32. doi: 10.1038/nbt.2647, PMID 23873081.

Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJM. Diversity of RISPR loci in Escherichia coli. Microbiology. 2010;156(5):1351–61. doi: 10.1099/mic.0.036046–0.

Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 2007;8(4):R61. doi: 10.1186/gb-2007–8–4-r61, PMID 17442114.

Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 2002;30(2):482–96. doi: 10.1093/nar/30.2.482, PMID 11788711.

Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 2011;30(7):1335–42. doi: 10.1038/emboj.2011.41, PMID 21343909.

Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468(7320):67–71. doi: 10.1038/nature09523, PMID 21048762.

Anantharaman V, Iyer LM, Aravind L. 2010. Presence of a classical RRM-fold palm domain in Thg1-type 3_–5_ nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains.Biol. Direct 5:43.

Rollins MF, Schuman JT, Paulus K, Bukhari HST, Wiedenheft B. Mechanismof foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa. Nucleic Acids Res. 2015;43(4):2216–22. doi: 10.1093/nar/gkv094.

Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature. 2015;519(7542):199–202. doi: 10.1038/nature14245, PMID 25707807.

Ronda C, Maury J, Jakociunas T, Jacobsen SA, Germann SM, Harrison SJ, Borodina I, Keasling JD, Jensen MK, Nielsen AT. CrEdit: CRISPR mediated multiloci gene integration in Saccharomyces cerevisiae. Microb Cell Factories. 2015;14:97.

Osakabe Y, Osakabe K. Genome editing with engineered nucleases in plants. Plant Cell Physiol. 2015;56(3):389–400. doi: 10.1093/pcp/pcu170, PMID 25416289.

Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T, Joung JK, Voytas DF. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A. 2010;107(26):12028–33. doi: 10.1073/pnas.0914991107, PMID 20508152.

Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol. 2013;31(8):686–8. doi: 10.1038/nbt.2650, PMID 23929338.

Shan Q, Wang Y, Li J, Gao C. Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc. 2014;9(10):2395–410. doi: 10.1038/nprot.2014.157, PMID 25232936.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23. doi: 10.1126/science.1231143, PMID 23287718.

Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823–6. doi: 10.1126/science.1232033, PMID 23287722.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23. doi: 10.1126/science.1231143, PMID 23287718.

Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823–6. doi: 10.1126/science.1232033, PMID 23287722.

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–83. doi: 10.1016/j.cell.2013.02.022, PMID 23452860.

Carroll D, Charo RA. The societal opportunities and challenges of genome editing. Genome Biol. 2015;16:242. doi: 10.1186/s13059–015–0812–0, PMID 26537374.

Wang Z. Genome engineering in cattle: recent technological advancements. Chromosome Res. 2015;23(1):17–29. doi: 10.1007/s10577–014–9452–6.

Grobet L, Martin LJ, Poncelet D, Pirottin D, Brouwers B, Riquet J, Schoeberlein A, Dunner S, Ménissier F, Massabanda J, Fries R, Hanset R, Georges M. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat Genet. 1997;17(1):71–4. doi: 10.1038/ng0997–71, PMID 9288100.

Proudfoot C, Carlson DF, Huddart R, Long CR, Pryor JH, King TJ, Lillico SG, Mileham AJ, McLaren DG, Whitelaw CB, Fahrenkrug SC. Genome edited sheep and cattle. Transgen Res. 2015;24(1):147–53. doi: 10.1007/s11248–014–9832-x, PMID 25204701.

Heo YT, Quan X, Xu YN, Baek S, Choi H, Kim NH, Kim J. CRISPR/Cas9 nuclease mediated gene knock-in bovine-induced pluripotent cells. Stem Cells Dev. 2015;24(3):393–402. doi: 10.1089/scd.2014.0278, PMID 25209165.

Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE. Rational design of highly active sgRNAs for CRISPRCas9-mediated gene inactivation. Nat Biotechnol. 2014;32(12):1262–7. doi: 10.1038/nbt.3026, PMID 25184501.

Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPRCas9. Nat Biotechnol. 2016;34(2):184–91. doi: 10.1038/nbt.3437, PMID 26780180.

Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. CRISPR/Cas9 systems have off-target activity with insertion or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 2014;42(11):7473–85. doi: 10.1093/nar/gku402, PMID 24838573.

Heigwer F, Kerr G, Boutros M. E-CRISP: fast CRISPR target site identification. Nat Methods. 2014;11(2):122–3. doi: 10.1038/nmeth.2812, PMID 24481216.

Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. CRISPR-P: aweb tool for synthetic single guide RNA design of CRISPR-system in plants. Mol Plant. 2014;7(9):1494–6. doi: 10.1093/mp/ssu044, PMID 24719468.

Ledford H. CRISPR, the disruptor. Nature. 2015;522(7554):20–4. doi: 10.1038/522020a, PMID 26040877.

Ma M, Ye AY, Zheng W, Kong L. A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. BioMed Res Int. 2013;2013:270805. doi: 10.1155/2013/270805.

Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics. 2015;31(22):3676–8. doi: 10.1093/bioinformatics/btv423, PMID 26209430.

Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154(6):1380–9. doi: 10.1016/j.cell.2013.08.021, PMID 23992846.

Webber BL, Raghu S, Edwards OR [opinion]. Opinion: Is CRISPR-based gene drive a biocontrol silver bullet or global conservation threat? Proc Natl Acad Sci U S A. 2015;112(34):10565–7. doi: 10.1073/pnas.1514258112, PMID 26272924.


Refbacks

  • There are currently no refbacks.