Abstract
Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.
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References
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315(5819):1709–1712. doi:10.1126/science.1138140
Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24(1):132–141. doi:10.1101/gr.162339.113
Dominguez AA, Lim WA, Qi LS (2016) Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 17(1):5–15. doi:10.1038/nrm.2015.2
Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32(3):279–284. doi:10.1038/nbt.2808
Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, Retterath A, Stoddard T, Juillerat A, Cedrone F, Mathis L, Voytas DF, Zhang F (2014) Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnol J 12(7):934–940. doi:10.1111/pbi.12201
Heigwer F, Kerr G, Boutros M (2014) E-CRISP: fast CRISPR target site identification. Nat Methods 11(2):122–123. doi:10.1038/nmeth.2812
Hendel A, Fine EJ, Bao G, Porteus MH (2015) Quantifying on- and off-target genome editing. Trends Biotechnol 33(2):132–140. doi:10.1016/j.tibtech.2014.12.001
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 (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31(9):827–832. doi:10.1038/nbt.2647
Jensen SP, Febres VJ, Moore GA (2014) Cell penetrating peptides as an alternative transformation method in citrus. J Pathol 1(1). Retrieved from: http://escholarship.org/uc/item/8hs6r4zj
Jones HD (2015) Regulatory uncertainty over genome editing. Nature Plants 1:14011. doi:10.1038/nplants.2014.11
Kanchiswamy CN, Malnoy M, Velasco R, Kim JS, Viola R (2015a) Non-GMO genetically edited crop plants. Trends Biotechnol 33(9):489–491. doi:10.1016/j.tibtech.2015.04.002
Kanchiswamy CN, Sargent DJ, Velasco R, Maffei ME, Malnoy M (2015b) Looking forward to genetically edited fruit crops. Trends Biotechnol 33(2):62–64. doi:10.1016/j.tibtech.2014.07.003
Kim H, Kim JS (2014) A guide to genome engineering with programmable nucleases. Nat Rev Genet 15(5):321–334. doi:10.1038/nrg3686
Kim E, Kim S, Kim DH, Choi BS, Choi IY, Kim JS (2012) Precision genome engineering with programmable DNA-nicking enzymes. Genome Res 22(7):1327–1333. doi:10.1101/gr.138792.112
Kim S, Kim D, Cho SW, Kim J, Kim JS (2014) Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24(6):1012–1019. doi:10.1101/gr.171322.113
Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523(7561):481–485. doi:10.1038/nature14592
Koo T, Lee J, Kim JS (2015) Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9. Mol Cells 38(6):475–481. doi:10.14348/molcells.2015.0103
Ledford H (2013) US regulation misses some GM crops. Nature 500(7463):389–390. doi:10.1038/500389a
Lee HJ, Kim E, Kim JS (2010) Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20(1):81–89. doi:10.1101/gr.099747.109
Lee HJ, Kweon J, Kim E, Kim S, Kim JS (2012) Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. Genome Res 22(3):539–548. doi:10.1101/gr.129635.111
Lee JS, Kwak SJ, Kim J, Kim AK, Noh HM, Kim JS, Yu K (2014) RNA-guided genome editing in Drosophila with the purified Cas9 protein. G3 4(7):1291–1295. doi:10.1534/g3.114.012179
Liu J, Gaj T, Yang Y, Wang N, Shui S, Kim S, Kanchiswamy CN, Kim JS, Barbas CF 3rd (2015) Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nat Protoc 10(11):1842–1859. doi:10.1038/nprot.2015.117
MacPherson CR, Scherf A (2015) Flexible guide-RNA design for CRISPR applications using Protospacer Workbench. Nat Biotechnol 33(8):805–806. doi:10.1038/nbt.3291
Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31(9):833–838. doi:10.1038/nbt.2675
Martin-Ortigosa S, Peterson DJ, Valenstein JS, Lin VS, Trewyn BG, Lyznik LA, Wang K (2014) Mesoporous silica nanoparticle-mediated intracellular Cre protein delivery for maize genome editing via loxP site excision. Plant Physiol 164(2):537–547. doi:10.1104/pp.113.233650
Masani MY, Noll GA, Parveez GK, Sambanthamurthi R, Prufer D (2014) Efficient transformation of oil palm protoplasts by PEG-mediated transfection and DNA microinjection. PLoS One 9(5):e96831. doi:10.1371/journal.pone.0096831
Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic acids research 42(Web Server issue):W401–W407. doi:10.1093/nar/gku410
Naito Y, Hino K, Bono H, Ui-Tei K (2015) CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31(7):1120–1123. doi:10.1093/bioinformatics/btu743
O’Brien A, Bailey TL (2014) GT-scan: identifying unique genomic targets. Bioinformatics 30(18):2673–2675. doi:10.1093/bioinformatics/btu354
Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW (2014) Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci USA 111(25):9253–9258. doi:10.1073/pnas.1323941111
Raitskin O, Patron NJ (2016) Multi-gene engineering in plants with RNA-guided Cas9 nuclease. Curr Opin Biotechnol 37:69–75. doi:10.1016/j.copbio.2015.11.008
Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6):1380–1389. doi:10.1016/j.cell.2013.08.021
Ren X, Yang Z, Mao D, Chang Z, Qiao HH, Wang X, Sun J, Hu Q, Cui Y, Liu LP, Ji JY, Xu J, Ni JQ (2014) Performance of the Cas9 nickase system in Drosophila melanogaster. Gfdfd 4(10):1955–1962. doi:10.1534/g3.114.013821
Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2015) Rationally engineered Cas9 nucleases with improved specificity. Science. doi:10.1126/science.aad5227
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE 10(4):e0124633. doi:10.1371/journal.pone.0124633
Subburaj S, Chung SJ, Lee C, Ryu SM, Kim DH, Kim JS, Bae S, Lee GJ (2016) Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Rep. doi:10.1007/s00299-016-1937-7
Waltz E (2012) Tiptoeing around transgenics. Nat Biotechnol 30(3):215–217. doi:10.1038/nbt.2143
Woo JW, Kim J, Kwon SI, Corvalan C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol 33(11):1162–1164. doi:10.1038/nbt.3389
Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, Zhang B (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics. doi:10.1093/bioinformatics/btt764
Xie S, Shen B, Zhang C, Huang X, Zhang Y (2014) sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS ONE 9(6):e100448. doi:10.1371/journal.pone.0100448
Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014) CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS One 9(9):e108424. doi:10.1371/journal.pone.0108424
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The author thank Daniel James Sargent and Massimo Maffei for contributing his time and efforts to proofread and improve this manuscript.
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Communicated by M. Mahfouz.
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Kanchiswamy, C.N. DNA-free genome editing methods for targeted crop improvement. Plant Cell Rep 35, 1469–1474 (2016). https://doi.org/10.1007/s00299-016-1982-2
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DOI: https://doi.org/10.1007/s00299-016-1982-2