Genome Editing Tools in Plants (2024)

1. Mohanta T.K., Bashir T., Hashem A., Abd_Allah E.F. Systems biology approach in plant abiotic stresses. Plant Physiol. Biochem. 2017;121:58–73. doi:10.1016/j.plaphy.2017.10.019. [PubMed] [CrossRef] [Google Scholar]

2. MacDonald I.C., Deans T.L. Tools and applications in synthetic biology. Pt AAdv. Drug Deliv. Rev. 2016;105:20–34. doi:10.1016/j.addr.2016.08.008. [PubMed] [CrossRef] [Google Scholar]

3. Paszkowski J., Baur M., Bogucki A., Potrykus I. Gene targeting in plants. EMBO J. 1988;7:4021–4026. [PMC free article] [PubMed] [Google Scholar]

4. Templeton N.S., Roberts D.D., Safer B. Efficient gene targeting in mouse embryonic stem cells. Gene Ther. 1997;4:700–709. doi:10.1038/sj.gt.3300457. [PubMed] [CrossRef] [Google Scholar]

5. Te Riele H., Maandag E.R., Berns A. Highly efficient gene targeting in embryonic stem cells through hom*ologous recombination with isogenic DNA constructs. Proc. Natl. Acad. Sci. USA. 1992;89:5128–5132. doi:10.1073/pnas.89.11.5128. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

6. Park S.-Y., Vaghchhipawala Z., Vasudevan B., Lee L.-Y., Shen Y., Singer K., Waterworth W.M., Zhang Z.J., West C.E., Mysore K.S., et al. Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-hom*ologous end-joining proteins. Plant J. 2015;81:934–946. doi:10.1111/tpj.12779. [PubMed] [CrossRef] [Google Scholar]

7. Wang N., Shi L. Screening of mutations by TILLING in plants BT—Plant genotyping: Methods and protocols. In: Batley J., editor. Plant Genotyping. Springer; New York, NY, USA: 2015. pp. 193–203. [PubMed] [Google Scholar]

8. Kurowska M., Daszkowska-Golec A., Gruszka D., Marzec M., Szurman M., Szarejko I., Maluszynski M. TILLING - a shortcut in functional genomics. J. Appl. Genet. 2011;52:371–390. doi:10.1007/s13353-011-0061-1. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

9. Henikoff S., Till B.J., Comai L. TILLING. Traditional Mutagenesis Meets Functional Genomics. Plant Physiol. 2004;135:630–636. doi:10.1104/pp.104.041061. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

10. Puchta H. Gene replacement by hom*ologous recombination in plants. Plant Mol. Biol. 2002;48:173–182. doi:10.1023/A:1013761821763. [PubMed] [CrossRef] [Google Scholar]

11. Puchta H., Dujon B., Hohn B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by hom*ologous recombination. Proc. Natl. Acad. Sci. USA. 1996;93:5055–5060. doi:10.1073/pnas.93.10.5055. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

12. Roy S. Maintenance of genome stability in plants: Repairing DNA double strand breaks and chromatin structure stability. Front. Plant Sci. 2014;5:487. doi:10.3389/fpls.2014.00487. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

13. Sung P., Klein H. Mechanism of hom*ologous recombination: Mediators and helicases take on regulatory functions. Nat. Rev. Mol. Cell Biol. 2006;7:739–750. doi:10.1038/nrm2008. [PubMed] [CrossRef] [Google Scholar]

14. Puchta H., Fauser F. Synthetic nucleases for genome engineering in plants: Prospects for a bright future. Plant J. 2014;78:727–741. doi:10.1111/tpj.12338. [PubMed] [CrossRef] [Google Scholar]

15. Fell V.L., Schild-Poulter C. The Ku heterodimer: Function in DNA repair and beyond. Mutat. Res. Mutat. Res. 2015;763:15–29. doi:10.1016/j.mrrev.2014.06.002. [PubMed] [CrossRef] [Google Scholar]

16. Walker J.R., Corpina R.A., Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 2001;412:607. doi:10.1038/35088000. [PubMed] [CrossRef] [Google Scholar]

17. Knoll A., Higgins J.D., Seeliger K., Reha S.J., Dangel N.J., Bauknecht M., Schröpfer S., Franklin F.C.H., Puchta H. The fanconi anemia ortholog FANCM ensures ordered hom*ologous recombination in both somatic and meiotic cells in Arabidopsis. Plant Cell. 2012;24:1448–1464. doi:10.1105/tpc.112.096644. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

18. Hartung F., Suer S., Bergmann T., Puchta H. The role of AtMUS81 in DNA repair and its genetic interaction with the helicase AtRecQ4A. Nucleic Acids Res. 2006;34:4438–4448. doi:10.1093/nar/gkl576. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

19. Rodriguez K., Wang Z., Friedberg E.C., Tomkinson A.E. Identification of functional domains within the RAD1.RAD10 repair and recombination endonuclease of Saccharomyces cerevisiae. J. Biol. Chem. 1996;271:20551–20558. doi:10.1074/jbc.271.34.20551. [PubMed] [CrossRef] [Google Scholar]

20. Mladenov E., Iliakis G. Induction and repair of DNA double strand breaks: The increasing spectrum of non-hom*ologous end joining pathways. Mutat. Res. Mol. Mech. Mutagen. 2011;711:61–72. doi:10.1016/j.mrfmmm.2011.02.005. [PubMed] [CrossRef] [Google Scholar]

21. Charbonnel C., Allain E., Gallego M.E., White C.I. Kinetic analysis of DNA double-strand break repair pathways in Arabidopsis. DNA Repair. 2011;10:611–619. doi:10.1016/j.dnarep.2011.04.002. [PubMed] [CrossRef] [Google Scholar]

22. Mengiste T., Paszkowski J. Prospects for the precise engineering of plant genomes by hom*ologous recombination. Biol. Chem. 1999;380:749–758. doi:10.1515/BC.1999.095. [PubMed] [CrossRef] [Google Scholar]

23. Liberman-Lazarovich M., Levy A. hom*ologous recombination in plants: An antireview. Methods Mol. Biol. 2011;701:51–65. [PubMed] [Google Scholar]

24. Petolino J.F. Genome editing in plants via designed zinc finger nucleases. Vitr. Cell. Dev. Biol. 2015;51:1–8. doi:10.1007/s11627-015-9663-3. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

25. Carroll D. Genome engineering with zinc-finger nucleases. Genetics. 2011;188:773–782. doi:10.1534/genetics.111.131433. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

26. Carlson D.F., Fahrenkrug S.C., Hackett P.B. Targeting DNA with fingers and TALENs. Mol. Ther. Nucleic Acids. 2012;1:e3. doi:10.1038/mtna.2011.5. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

27. Gupta A., Christensen R.G., Rayla A.L., Lakshmanan A., Stormo G.D., Wolfe S.A. An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods. 2012;9:588–590. doi:10.1038/nmeth.1994. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

28. Pabo C.O., Peisach E., Grant R.A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 2001;70:313–340. doi:10.1146/annurev.biochem.70.1.313. [PubMed] [CrossRef] [Google Scholar]

29. Thakore P.I., Gersbach C.A. Genome engineering for therapeutic applications. In: Laurence J., Franklin N., editors. Translating Gene Therapy to the Clinic. Academic Press; Boston, MA, USA: 2015. pp. 27–43. [Google Scholar]

30. Pavletich N.P., Pabo C.O. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A. Science. 1991;252:809–817. doi:10.1126/science.2028256. [PubMed] [CrossRef] [Google Scholar]

31. Elrod-Erickson M., Pabo C.O. Binding Studies with mutants of Zif268: Contribution of individual side chains to binding affinity and specificity in the ZIF268 zinc finger-DNA complex. J. Biol. Chem. 1999;274:19281–19285. doi:10.1074/jbc.274.27.19281. [PubMed] [CrossRef] [Google Scholar]

32. Shi Y., Berg J.M. A direct comparison of the properties of natural and designed zinc-finger proteins. Chem. Biol. 1995;2:83–89. doi:10.1016/1074-5521(95)90280-5. [PubMed] [CrossRef] [Google Scholar]

33. Liu Q., Segal D.J., Ghiara J.B., Barbas C.F. Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc. Natl. Acad. Sci. USA. 1997;94:5525–5530. doi:10.1073/pnas.94.11.5525. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

34. Beerli R.R., Segal D.J., Dreier B., Barbas C.F. Toward controlling gene expression at will: Specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc. Natl. Acad. Sci. USA. 1998;95:14628–14633. doi:10.1073/pnas.95.25.14628. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

35. Kim J.-S., Pabo C.O. Getting a handhold on DNA: Design of poly-zinc finger proteins with femtomolar dissociation constants. Proc. Natl. Acad. Sci. USA. 1998;95:2812–2817. doi:10.1073/pnas.95.6.2812. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

36. Kim Y.G., Cha J., Chandrasegaran S. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. USA. 1996;93:1156–1160. doi:10.1073/pnas.93.3.1156. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

37. Smith J., Bibikova M., Whitby F.G., Reddy A.R., Chandrasegaran S., Carroll D. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res. 2000;28:3361–3369. doi:10.1093/nar/28.17.3361. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

38. Mani M., Kandavelou K., Dy F.J., Durai S., Chandrasegaran S. Design, engineering, and characterization of zinc finger nucleases. Biochem. Biophys. Res. Commun. 2005;335:447–457. doi:10.1016/j.bbrc.2005.07.089. [PubMed] [CrossRef] [Google Scholar]

39. Alwin S., Gere M.B., Guhl E., Effertz K., Barbas C.F., Segal D.J., Weitzman M.D., Cathomen T. Custom zinc-finger nucleases for use in human cells. Mol. Ther. 2005;12:610–617. doi:10.1016/j.ymthe.2005.06.094. [PubMed] [CrossRef] [Google Scholar]

40. Liu Q., Zia Z., Case C. Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem. 2001;277:3850–3856. doi:10.1074/jbc.M110669200. [PubMed] [CrossRef] [Google Scholar]

41. Dreier B., Beerli R.R., Segal D.J., Flippin J.D., Barbas C.F. Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J. Biol. Chem. 2001;276:29466–29478. doi:10.1074/jbc.M102604200. [PubMed] [CrossRef] [Google Scholar]

42. Dreier B., Segal D.J., Barbas C.F. Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains. J. Mol. Biol. 2000;303:489–502. doi:10.1006/jmbi.2000.4133. [PubMed] [CrossRef] [Google Scholar]

43. Dreier B., Fuller R.P., Segal D.J., Lund C.V., Blancafort P., Huber A., Koksch B., Barbas C.F. Development of zinc finger domains for recognition of the 5’-CNN-3’ family DNA sequences and their use in the construction of artificial transcription factors. J. Biol. Chem. 2005;280:35588–35597. doi:10.1074/jbc.M506654200. [PubMed] [CrossRef] [Google Scholar]

44. Jamieson A.C., Miller J.C., Pabo C.O. Drug discovery with engineered zinc-finger proteins. Nat. Rev. Drug. Discov. 2003;2:361–368. doi:10.1038/nrd1087. [PubMed] [CrossRef] [Google Scholar]

45. Pavletich N.P., Pabo C.O. Crystal structure of a five-finger GLI-DNA complex: New perspectives on zinc fingers. Science. 1993;261:1701–1707. doi:10.1126/science.8378770. [PubMed] [CrossRef] [Google Scholar]

46. Greisman H.A., Pabo C.O. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science. 1997;275:657–661. doi:10.1126/science.275.5300.657. [PubMed] [CrossRef] [Google Scholar]

47. Durai S., Mani M., Kandavelou K., Wu J., Porteus M.H., Chandrasegaran S. Zinc finger nucleases: Custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res. 2005;33:5978–5990. doi:10.1093/nar/gki912. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

48. Mani M., Smith J., Kandavelou K., Berg J.M., Chandrasegaran S. Binding of two zinc finger nuclease monomers to two specific sites is required for effective double-strand DNA cleavage. Biochem. Biophys. Res. Commun. 2005;334:1191–1197. doi:10.1016/j.bbrc.2005.07.021. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

49. Porteus M.H. Mammalian gene targeting with designed zinc finger nucleases. Mol. Ther. 2006;13:438–446. doi:10.1016/j.ymthe.2005.08.003. [PubMed] [CrossRef] [Google Scholar]

50. Durai S., Bosley A., Abulencia A.B., Chandrasegaran S., Ostermeier M. A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. Comb. Chem. High Throughput Screen. 2006;9:301–311. doi:10.2174/138620706776843147. [PubMed] [CrossRef] [Google Scholar]

51. Joung J.K., Sander J.D. TALENs: A widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 2013;14:49–55. doi:10.1038/nrm3486. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

52. Bonas U., Stall R.E., Staskawicz B. Genetic and structural characterization of the avirulence gene avrBs3 from Xanthom*onas campestris pv. vesicatoria. Mol. Gen. Genet. MGG. 1989;218:127–136. doi:10.1007/BF00330575. [PubMed] [CrossRef] [Google Scholar]

53. Boch J., Bonas U. Xanthom*onas AvrBs3 family-type III effectors: Discovery and function. Annu. Rev. Phytopathol. 2010;48:419–436. doi:10.1146/annurev-phyto-080508-081936. [PubMed] [CrossRef] [Google Scholar]

54. Bitinaite J., Wah D.A., Aggarwal A.K., Schildkraut I. FokI dimerization is required for DNA cleavage. Proc. Natl. Acad. Sci. USA. 1998;95:10570–10575. doi:10.1073/pnas.95.18.10570. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

55. Wah D.A., Bitinaite J., Schildkraut I., Aggarwal A.K. Structure of FokI has implications for DNA cleavage. Proc. Natl. Acad. Sci. USA. 1998;95:10564–10569. doi:10.1073/pnas.95.18.10564. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

56. Li T., Liu B., Spalding M.H., Weeks D.P., Yang B. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat. Biotechnol. 2012;30:390–392. doi:10.1038/nbt.2199. [PubMed] [CrossRef] [Google Scholar]

57. Cermak T., Doyle E.L., Christian M., Wang L., Zhang Y., Schmidt C., Baller J.A., Somia N.V., Bogdanove A.J., Bogdanove A.J., Voytas D.F. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011;39:e82. doi:10.1093/nar/gkr218. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

58. Small I.D., Rackham O., Filipovska A. Organelle transcriptomes: Products of a deconstructed genome. Curr. Opin. Microbiol. 2013;16:652–658. doi:10.1016/j.mib.2013.07.011. [PubMed] [CrossRef] [Google Scholar]

59. Schmitz-Linneweber C., Small I. Pentatricopeptide repeat proteins: A socket set for organelle gene expression. Trends Plant Sci. 2008;13:663–670. doi:10.1016/j.tplants.2008.10.001. [PubMed] [CrossRef] [Google Scholar]

60. Barkan A., Small I. Pentatricopeptide repeat proteins in plants. Annu. Rev. Plant Biol. 2014;65:415–442. doi:10.1146/annurev-arplant-050213-040159. [PubMed] [CrossRef] [Google Scholar]

61. Okuda K., Myouga F., Motohashi R., Shinozaki K., Shikanai T. Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc. Natl. Acad. Sci. USA. 2007;104:8178–8183. doi:10.1073/pnas.0700865104. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

62. Shikanai T. RNA editing in plant organelles: Machinery, physiological function and evolution. Cell. Mol. Life Sci. C. 2006;63:698–708. doi:10.1007/s00018-005-5449-9. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

63. Lurin C., Andrés C., Aubourg S., Bellaoui M., Bitton F., Bruyère C., Caboche M., Debast C., Gualberto J., Hoffmann B., et al. Genome-Wide Analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 2004;16:2089–2103. doi:10.1105/tpc.104.022236. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

64. Boussardon C., Avon A., Kindgren P., Bond C.S., Challenor M., Lurin C., Small I. The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1. New Phytol. 2014;203:1090–1095. doi:10.1111/nph.12928. [PubMed] [CrossRef] [Google Scholar]

65. Barkan A., Rojas M., Fujii S., Yap A., Chong Y.S., Bond C.S., Small I. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet. 2012;8:e1002910. doi:10.1371/journal.pgen.1002910. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

66. Manna S. An overview of pentatricopeptide repeat proteins and their applications. Biochimie. 2015;113:93–99. doi:10.1016/j.biochi.2015.04.004. [PubMed] [CrossRef] [Google Scholar]

67. Yin P., Li Q., Yan C., Liu Y., Liu J., Yu F., Wang Z., Long J., He J., Wang H.-W., et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013;504:168–171. doi:10.1038/nature12651. [PubMed] [CrossRef] [Google Scholar]

68. Yagi Y., Hayashi S., Kobayashi K., Hirayama T., Nakamura T. Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants. PLoS ONE. 2013;8:e57286. doi:10.1371/journal.pone.0057286. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

69. Fujii S., Bond C.S., Small I.D. Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc. Natl. Acad. Sci. USA. 2011;108:1723–1728. doi:10.1073/pnas.1007667108. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

70. O’Toole N., Hattori M., Andres C., Iida K., Lurin C., Schmitz-Linneweber C., Sugita M., Small I. On the expansion of the pentatricopeptide repeat gene family in plants. Mol. Biol. Evol. 2008;25:1120–1128. doi:10.1093/molbev/msn057. [PubMed] [CrossRef] [Google Scholar]

71. De Longevialle A.F., Hendrickson L., Taylor N.L., Delannoy E., Lurin C., Badger M., Millar A.H., Small I. The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana. Plant J. 2008;56:157–168. doi:10.1111/j.1365-313X.2008.03581.x. [PubMed] [CrossRef] [Google Scholar]

72. Zoschke R., Kroeger T., Belcher S., Schöttler M.A., Barkan A., Schmitz-Linneweber C. The pentatricopeptide repeat-SMR protein ATP4 promotes translation of the chloroplast atpB/E mRNA. Plant J. 2012;72:547–558. doi:10.1111/j.1365-313X.2012.05081.x. [PubMed] [CrossRef] [Google Scholar]

73. Zoschke R., Qu Y., Zubo Y.O., Börner T., Schmitz-Linneweber C. Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana. J. Plant Res. 2013;126:403–414. doi:10.1007/s10265-012-0527-1. [PubMed] [CrossRef] [Google Scholar]

74. Liu S., Melonek J., Boykin L.M., Small I., Howell K.A. PPR-SMRs: Ancient proteins with enigmatic functions. RNA Biol. 2013;10:1501–1510. doi:10.4161/rna.26172. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

75. Sander J.D., Joung J.K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 2014;32:347–355. doi:10.1038/nbt.2842. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

76. 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. USA. 2012;109:E2579–E2586. doi:10.1073/pnas.1208507109. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

77. Hsu P.D., Scott D.A., Weinstein J.A., Ran F.A., Konermann S., Agarwala V., Li Y., Fine E.J., Wu X., Shalem O., et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013;31:827–832. doi:10.1038/nbt.2647. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

78. Bortesi L., Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol. Adv. 2015;33:41–52. doi:10.1016/j.biotechadv.2014.12.006. [PubMed] [CrossRef] [Google Scholar]

79. Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–823. doi:10.1126/science.1231143. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

80. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., Norville J.E., Church G.M. RNA-Guided human genome engineering via Cas9. Science. 2013;339:823–826. doi:10.1126/science.1232033. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

81. Liu Y., Ma S., Wang X., Chang J., Gao J., Shi R., Zhang J., Lu W., Liu Y., Zhao P., et al. Highly efficient multiplex targeted mutagenesis and genomic structure variation in Bombyx mori cells using CRISPR/Cas9. Insect Biochem. Mol. Biol. 2014;49:35–42. doi:10.1016/j.ibmb.2014.03.010. [PubMed] [CrossRef] [Google Scholar]

82. Xie K., Yang Y. RNA-Guided Genome editing in plants using a CRISPR–Cas system. Mol. Plant. 2013;6:1975–1983. doi:10.1093/mp/sst119. [PubMed] [CrossRef] [Google Scholar]

83. Feng Z., Mao Y., Xu N., Zhang B., Wei P., Yang D., Wang Z. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc. Natl. Acad. Sci. USA. 2014;111:4632–4637. doi:10.1073/pnas.1400822111. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

84. Jia H., Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS ONE. 2014;9:e93806. doi:10.1371/journal.pone.0093806. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

85. Li J.-F., Aach J., Norville J.E., McCormack M., Zhang D., Bush J., Church G.M., Sheen J. Multiplex and hom*ologous recombination-mediated plant genome editing via guide RNA/Cas9. Nat. Biotechnol. 2013;31:688–691. doi:10.1038/nbt.2654. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

86. Nekrasov V., Staskawicz B., Weigel D., Jones J.D.G., Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013;31:691–693. doi:10.1038/nbt.2655. [PubMed] [CrossRef] [Google Scholar]

87. Shan Q., Wang Y., Li J., Zhang Y., Chen K., Liang Z., Zhang K., Liu J., Xi J.J., Qiu J.-L., et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol. 2013;31:686–688. doi:10.1038/nbt.2650. [PubMed] [CrossRef] [Google Scholar]

88. Upadhyay S.K., Kumar J., Alok A., Tuli R. RNA-guided genome editing for target gene mutations in wheat. G3. 2013;3:2233–2238. doi:10.1534/g3.113.008847. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

89. Zhou H., Liu B., Weeks D.P., Spalding M.H., Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 2014;42:10903–10914. doi:10.1093/nar/gku806. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

90. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013;31:233–239. doi:10.1038/nbt.2508. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

91. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–821. doi:10.1126/science.1225829. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

92. Pattanayak V., Lin S., Guilinger J.P., Ma E., Doudna J.A., Liu D.R. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 2013;31:839–843. doi:10.1038/nbt.2673. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

93. Fu Y., Foden J.A., Khayter C., Maeder M.L., Reyon D., Joung J.K., Sander J.D. High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 2013;31:822–826. doi:10.1038/nbt.2623. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

94. Lin Y., Cradick T.J., Brown M.T., Deshmukh H., Ranjan P., Sarode N., Wile B.M., Vertino P.M., Stewart F.J., Bao G. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 2014;42:7473–7485. doi:10.1093/nar/gku402. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

95. sem*nova E., Jore M.M., Datsenko K.A., sem*nova A., Westra E.R., Wanner B., van der Oost J., Brouns S.J.J., Severinov K. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl. Acad. Sci. USA. 2011;108:10098–10103. doi:10.1073/pnas.1104144108. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

96. Cho S.W., Kim S., Kim Y., Kweon J., Kim H.S., Bae S., Kim J.-S. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24:132–141. doi:10.1101/gr.162339.113. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

97. Ran F.A., Hsu P.D., Lin C.-Y., Gootenberg J.S., Konermann S., Trevino A., Scott D.A., Inoue A., Matoba S., Zhang Y., et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154:1380–1389. doi:10.1016/j.cell.2013.08.021. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

98. Fu Y., Sander J.D., Reyon D., Cascio V.M., Joung J.K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 2014;32:279–284. doi:10.1038/nbt.2808. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

99. Mali P., Aach J., Stranges P.B., Esvelt K.M., Moosburner M., Kosuri S., Yang L., Church G.M. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 2013;31:833–838. doi:10.1038/nbt.2675. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

100. Miao J., Guo D., Zhang J., Huang Q., Qin G., Zhang X., Wan J., Gu H., Qu L.-J. Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res. 2013;23:1233–1236. doi:10.1038/cr.2013.123. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

101. Gao J., Wang G., Ma S., Xie X., Wu X., Zhang X., Wu Y., Zhao P., Xia Q. CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol. Biol. 2015;87:99–110. doi:10.1007/s11103-014-0263-0. [PubMed] [CrossRef] [Google Scholar]

102. Lindsay C.R., Roth D.B. An Unbiased method for detection of genome-wide off-target effects in cell lines treated with zinc finger nucleases. In: Storici F., editor. Gene Correction. Humana Press; Totowa, NJ, USA: 2014. pp. 353–369. [PubMed] [Google Scholar]

103. Kleinstiver B.P., Prew M.S., Tsai S.Q., Topkar V.V., Nguyen N.T., Zheng Z., Gonzales A.P.W., Li Z., Peterson R.T., Yeh J.-R. J., et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015;523:481–485. doi:10.1038/nature14592. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

104. Kleinstiver B.P., Pattanayak V., Prew M.S., Tsai S.Q., Nguyen N., Zheng Z., Joung J.K. High-fidelity CRISPR-Cas9 variants with undetectable genome-wide off-targets. Nature. 2016;529:490–495. doi:10.1038/nature16526. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

105. Slaymaker I.M., Gao L., Zetsche B., Scott D.A., Yan W.X., Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science. 2016;351:84–88. doi:10.1126/science.aad5227. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

106. Gilbert L.A., Larson M.H., Morsut L., Liu Z., Brar G.A., Torres S.E., Stern-Ginossar N., Brandman O., Whitehead E.H., Doudna J.A., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154:442–451. doi:10.1016/j.cell.2013.06.044. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

107. Maeder M.L., Linder S.J., Cascio V.M., Fu Y., Ho Q.H., Joung J.K. CRISPR RNA-guided activation of endogenous human genes. Nat Meth. 2013;10:977–979. doi:10.1038/nmeth.2598. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

108. Bikard D., Marraffini L.A. Control of gene expression by CRISPR-Cas systems. F1000Prime Rep. 2013;5:47. doi:10.12703/P5-47. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

109. Piatek A., Ali Z., Baazim H., Li L., Abulfaraj A., Al-Shareef S., Aouida M., Mahfouz M.M. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol. J. 2015;13:578–589. doi:10.1111/pbi.12284. [PubMed] [CrossRef] [Google Scholar]

110. Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173–1183. doi:10.1016/j.cell.2013.02.022. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

111. Esvelt K.M., Mali P., Braff J.L., Moosburner M., Yaung S.J., Church G.M. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods. 2013;10:1116–1121. doi:10.1038/nmeth.2681. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

112. Anton T., Bultmann S., Leonhardt H., Markaki Y. Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system. Nucleus. 2014;5:163–172. doi:10.4161/nucl.28488. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

113. Maeder M.L., Angstman J.F., Richardson M.E., Linder S.J., Cascio V.M., Tsai S.Q., Ho Q.H., Sander J.D., Reyon D., Bernstein B.E., et al. Targeted DNA demethylation and endogenous gene activation using programmable TALE-TET1 fusions. Nat. Biotechnol. 2013;31:1137–1142. doi:10.1038/nbt.2726. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

114. Nishida K., Arazoe T., Yachie N., Banno S., Kakimoto M., Tabata M., Mochizuki M., Miyabe A., Araki M., Hara K.Y., et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science. 2016 doi:10.1126/science.aaf8729. [PubMed] [CrossRef] [Google Scholar]

115. Lu Y., Zhu J.-K. Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Mol. Plant. 2017;10:523–525. doi:10.1016/j.molp.2016.11.013. [PubMed] [CrossRef] [Google Scholar]

116. Zong Y., Wang Y., Li C., Zhang R., Chen K., Ran Y., Qiu J.-L., Wang D., Gao C. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 2017;35:438–440. doi:10.1038/nbt.3811. [PubMed] [CrossRef] [Google Scholar]

117. Gaudelli N.M., Komor A.C., Rees H.A., Packer M.S., Badran A.H., Bryson D.I., Liu D.R. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017:1–27. doi:10.1038/nature24644. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

118. Small I. RNAi for revealing and engineering plant gene functions. Curr. Opin. Biotechnol. 2007;18:148–153. doi:10.1016/j.copbio.2007.01.012. [PubMed] [CrossRef] [Google Scholar]

119. Waterhouse P.M., Helliwell C.A. Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 2003;4:29–38. doi:10.1038/nrg982. [PubMed] [CrossRef] [Google Scholar]

120. Axtell M.J., Jan C., Rajagopalan R., Bartel D.P. A two-hit trigger for siRNA biogenesis in plants. Cell. 2006;127:565–577. doi:10.1016/j.cell.2006.09.032. [PubMed] [CrossRef] [Google Scholar]

121. Agrawal N., Dasaradhi P.V.N., Mohmmed A., Malhotra P., Bhatnagar R.K., Mukherjee S.K. RNA Interference: Biology, mechanism, and applications. Microbiol. Mol. Biol. Rev. 2003;67:657–685. doi:10.1128/MMBR.67.4.657-685.2003. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

122. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science. 2003;301:336–338. doi:10.1126/science.1085242. [PubMed] [CrossRef] [Google Scholar]

123. Seto A.G., Kingston R.E., Lau N.C. The coming of age for Piwi proteins. Mol. Cell. 2007;26:603–609. doi:10.1016/j.molcel.2007.05.021. [PubMed] [CrossRef] [Google Scholar]

124. Siomi M.C., Sato K., Pezic D., Aravin A.A. PIWI-interacting small RNAs: The vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 2011;12:246–258. doi:10.1038/nrm3089. [PubMed] [CrossRef] [Google Scholar]

125. Klattenhoff C., Theurkauf W. Biogenesis and germline functions of piRNAs. Development. 2008;135:3–9. doi:10.1242/dev.006486. [PubMed] [CrossRef] [Google Scholar]

126. Jackson A.L., Burchard J., Schelter J., Chau B.N., Cleary M., Lim L., Linsley P.S. Widspread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA. 2006;12:1179–1187. doi:10.1261/rna.25706. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

127. Birmingham A., Anderson E., Sullivan K., Reynolds A., Boese Q., Leake D., Karpilow J., Khvorova A. A protocol for designing siRNAs with high functionality and specificity. Nat. Protoc. 2007;2:2068–2078. doi:10.1038/nprot.2007.278. [PubMed] [CrossRef] [Google Scholar]

128. Meister G. Argonaute proteins: Functional insights and emerging roles. Nat. Rev. Genet. 2013;14:447–459. doi:10.1038/nrg3462. [PubMed] [CrossRef] [Google Scholar]

129. Hutvagner G., Simard M.J. Argonaute proteins: Key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 2008;9:22–32. doi:10.1038/nrm2321. [PubMed] [CrossRef] [Google Scholar]

130. Pratt A.J., MacRae I.J. The RNA-induced silencing complex: A versatile gene-silencing machine. J. Biol. Chem. 2009;284:17897–17901. doi:10.1074/jbc.R900012200. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

131. Redfern A.D., Colley S.M., Beveridge D.J., Ikeda N., Epis M.R., Li X., Foulds C.E., Stuart L.M., Barker A., Russell V.J., et al. RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators. Proc. Natl. Acad. Sci. USA. 2013;110:6536–6541. doi:10.1073/pnas.1301620110. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

132. Iki T., Ishikawa M., Yoshikawa M. In vitro formation of plant rna-induced silencing complexes using an extract of evacuolated tobacco protoplasts. In: Carbonell A., editor. Plant Argonaute Proteins. Springer; New York, NY, USA: 2017. pp. 39–53. [PubMed] [Google Scholar]

133. Kawamata T., Tomari Y. Making RISC. Trends Biochem. Sci. 2010;35:368–376. doi:10.1016/j.tibs.2010.03.009. [PubMed] [CrossRef] [Google Scholar]

134. Zhou H.-L., Luo G., Wise J.A., Lou H. Regulation of alternative splicing by local histone modifications: Potential roles for RNA-guided mechanisms. Nucleic Acids Res. 2014;42:701–713. doi:10.1093/nar/gkt875. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

135. Xie M., Yu B. siRNA-directed DNA methylation in plants. Curr. Genom. 2015;16:23–31. doi:10.2174/1389202915666141128002211. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

136. Kawasaki H., Taira K. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature. 2004;431:211–217. doi:10.1038/nature02889. [PubMed] [CrossRef] [Google Scholar]

137. Zhu H., Zhou Y., Castillo-González C., Lu A., Ge C., Zhao Y.-T., Duan L., Li Z., Axtell M.J., Wang X.-J., Zhang X. Bi-directional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat. Struct. Mol. Biol. 2013;20:1106–1115. doi:10.1038/nsmb.2646. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

138. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002;16:1616–1626. doi:10.1101/gad.1004402. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

139. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An Abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 2001;294:858–862. doi:10.1126/science.1065062. [PubMed] [CrossRef] [Google Scholar]

140. Kurzynska-Kokorniak A., Koralewska N., Pokornowska M., Urbanowicz A., Tworak A., Mickiewicz A., Figlerowicz M. The many faces of Dicer: The complexity of the mechanisms regulating Dicer gene expression and enzyme activities. Nucleic Acids Res. 2015;43:4365–4380. doi:10.1093/nar/gkv328. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

141. Kurihara Y., Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA. 2004;101:12753–12758. doi:10.1073/pnas.0403115101. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

142. Lu R., Martin-Hernandez A.M., Peart J.R., Malcuit I., Baulcombe D.C. Virus-induced gene silencing in plants. Methods. 2003;30:296–303. doi:10.1016/S1046-2023(03)00037-9. [PubMed] [CrossRef] [Google Scholar]

143. Lange M., Yellina A.L., Orashakova S., Becker A. virus-induced gene silencing (VIGS) in plants: An Overview of target species and the virus-derived vector systems. In: Becker A., editor. Virus-Induced Gene Silencing. Humana Press; Totowa, NJ, USA: 2013. pp. 1–14. [PubMed] [Google Scholar]

144. Burch-Smith T.M., Schiff M., Liu Y., Dinesh-Kumar S.P. Efficient virus-induced gene silencing in Arabidopsis. Plant Physiol. 2006;142:21–27. doi:10.1104/pp.106.084624. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

145. Warnefors M., Liechti A., Halbert J., Valloton D., Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol. 2014;15:R83. doi:10.1186/gb-2014-15-6-r83. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

146. Zhang B., Pan X., Cannon C.H., Cobb G.P., Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 2006;46:243–259. doi:10.1111/j.1365-313X.2006.02697.x. [PubMed] [CrossRef] [Google Scholar]

147. Li A., Mao L. Evolution of plant microRNA gene families. Cell Res. 2007;17:212–218. doi:10.1038/sj.cr.7310113. [PubMed] [CrossRef] [Google Scholar]

148. Tiwari M., Sharma D., Trivedi P.K. Artificial microRNA mediated gene silencing in plants: Progress and perspectives. Plant Mol. Biol. 2014;86:1–18. doi:10.1007/s11103-014-0224-7. [PubMed] [CrossRef] [Google Scholar]

149. Ossowski S., Schwab R., Weigel D. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 2008;53:674–690. doi:10.1111/j.1365-313X.2007.03328.x. [PubMed] [CrossRef] [Google Scholar]

150. Gasparis S., Kała M., Przyborowski M., Orczyk W., Nadolska-Orczyk A. Artificial MicroRNA-based specific gene silencing of grain hardness genes in polyploid cereals appeared to be not stable over transgenic plant generations. Front. Plant Sci. 2017;7:2017. doi:10.3389/fpls.2016.02017. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

151. Fujii S., Small I. The evolution of RNA editing and pentatricopeptide repeat genes. New Phytol. 2011;191:37–47. doi:10.1111/j.1469-8137.2011.03746.x. [PubMed] [CrossRef] [Google Scholar]

152. Iyer L.M., Zhang D., Rogozin I.B., Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res. 2011;39:9473–9497. doi:10.1093/nar/gkr691. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

153. Koito A., Ikeda T. Apolipoprotein B mRNA-editing, catalytic polypeptide cytidine deaminases and retroviral restriction. Wiley Interdiscip. Rev. RNA. 2012;3:529–541. doi:10.1002/wrna.1117. [PubMed] [CrossRef] [Google Scholar]

154. Teng B.-B., Ochsner S., Zhang Q., Soman K.V., Lau P.P., Chan L. Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): Structure–function relationships of RNA editing and dimerization. J. Lipid Res. 1999;40:623–635. [PubMed] [Google Scholar]

155. Yoshinaga K., Iinuma H., Masuzawa T., Uedal K. Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. Nucleic Acids Res. 1996;24:1008–1014. doi:10.1093/nar/24.6.1008. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

156. Papaioannou I., Simons J.P., Owen J.S. Oligonucleotide-directed gene-editing technology: Mechanisms and future prospects. Expert Opin. Biol. Ther. 2012;12:329–342. doi:10.1517/14712598.2012.660522. [PubMed] [CrossRef] [Google Scholar]

157. Tan S., Evans R.R., Dahmer M.L., Singh B.K., Shaner D.L. Imidazolinone-tolerant crops: History, current status and future. Pest. 2005;61:246–257. doi:10.1002/ps.993. [PubMed] [CrossRef] [Google Scholar]

158. Hartung F., Schiemann J., Quedlinburg D. Precise plant breeding using new genome editing techniques: Opportunities, safety and regulation in the EU. Plant J. 2014;78:742–752. doi:10.1111/tpj.12413. [PubMed] [CrossRef] [Google Scholar]

159. Hou H., Atlihan N., Lu Z.-X. New biotechnology enhances the application of cisgenesis in plant breeding. Front. Plant Sci. 2014;5:389. doi:10.3389/fpls.2014.00389. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

160. Schouten H.J., Krens F.A., Jacobsen E. Do cisgenic plants warrant less stringent oversight? Nat. Biotechnol. 2006;24:753. doi:10.1038/nbt0706-753. [PubMed] [CrossRef] [Google Scholar]

161. Holme I.B., Wendt T., Holm P.B. Intragenesis and cisgenesis as alternatives to transgenic crop development. Plant Biotechnol. J. 2013;11:395–407. doi:10.1111/pbi.12055. [PubMed] [CrossRef] [Google Scholar]

162. Gadaleta A., Giancaspro A., Blechl A.E., Blanco A. A transgenic durum wheat line that is free of marker genes and expresses 1Dy10. J. Cereal Sci. 2008;48:439–445. doi:10.1016/j.jcs.2007.11.005. [CrossRef] [Google Scholar]

163. Han K.M., Dharmawardhana P., Arias R.S., Ma C., Busov V., Strauss S.H. Gibberellin-associated cisgenes modify growth, stature and wood properties in Populus. Plant Biotechnol. J. 2011;9:162–178. doi:10.1111/j.1467-7652.2010.00537.x. [PubMed] [CrossRef] [Google Scholar]

164. Martin W., Rujan T., Richly E., Hansen A., Cornelsen S., Lins T., Leister D., Stoebe B., Hasegawa M., Penny D. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA. 2002;99:12246–12251. doi:10.1073/pnas.182432999. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

165. Lilly J.W., Havey M.J., Jackson S.A., Jiang J. Cytogenomic Analyses Reveal the Structural Plasticity of the Chloroplast Genome in Higher Plants. Plant Cell. 2001;13:245–254. doi:10.1105/tpc.13.2.245. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

166. Scharff L., Koop H. Linear molecules of tobacco ptDNA end at known replication origins and additional loci. Plant Mol. Biol. 2006:611–621. doi:10.1007/s11103-006-9042-x. [PubMed] [CrossRef] [Google Scholar]

167. Day A., Madesis P. DNA replication, recombination, and repair in plastids BT - cell and molecular biology of plastids. In: Bock R., editor. Cell and Molecular Biology of Plastids. Springer; Berlin/Heidelberg, Germany: 2007. pp. 65–119. [Google Scholar]

168. Daniell H., Lin C.-S., Yu M., Chang W.-J. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol. 2016;17:134. doi:10.1186/s13059-016-1004-2. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

169. Shi C., Wang S., Xia E.-H., Jiang J.-J., Zeng F.-C., Gao L.-Z. Full transcription of the chloroplast genome in photosynthetic eukaryotes. Sci. Rep. 2016;6:30135. doi:10.1038/srep30135. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

170. Scharff L.B., Bock R. Synthetic biology in plastids. Plant J. 2014;78:783–798. doi:10.1111/tpj.12356. [PubMed] [CrossRef] [Google Scholar]

171. Barkan A. Expression of plastid genes: Organelle-specific elaborations on a prokaryotic scaffold. Plant Physiol. 2011;155:1520–1532. doi:10.1104/pp.110.171231. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

172. Hofmann N.R. Regulation of plastid gene expression in the chloroplast-to-chromoplast transition. Plant Cell. 2008;20:823. doi:10.1105/tpc.108.200413. [CrossRef] [Google Scholar]

173. Babiychuk E., Vandepoele K., Wissing J., Garcia-Diaz M., De Rycke R., Akbari H., Joubès J., Beeckman T., Jänsch L., Frentzen M., Van Montagu M.C.E., Kushnir S. Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family. Proc. Natl. Acad. Sci. USA. 2011;108:6674–6679. doi:10.1073/pnas.1103442108. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

174. Bräutigam K., Dietzel L., Pfannschmidt T. Plastid-nucleus communication: Anterograde and retrograde signalling inthe development and function of plastids. In: Bock R., editor. Cell and Molecular Biology of Plastids. Springer; Berlin/Heidelberg, Germany: 2007. pp. 409–455. [Google Scholar]

175. Verhounig A., Karcher D., Bock R. Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc. Natl. Acad. Sci. USA. 2010;107:6204–6209. doi:10.1073/pnas.0914423107. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

176. Lu Y., Rijzaani H., Karcher D., Ruf S., Bock R. Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons. Proc. Natl. Acad. Sci. USA. 2013;110 doi:10.1073/pnas.1216898110. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

177. Elghabi Z., Ruf S., Bock R. Biolistic co-transformation of the nuclear and plastid genomes. Plant J. 2011;67:941–948. doi:10.1111/j.1365-313X.2011.04631.x. [PubMed] [CrossRef] [Google Scholar]

Genome Editing Tools in Plants (2024)

FAQs

What tools are used to genetically modify plants? ›

Genetic Engineering
  • Microbial Vectors. Agrobacterium tumefaciens is a naturally occurring soil microbe best known for causing crown gall disease on susceptible plant species. ...
  • Microprojectile Bombardment. ...
  • Electroporation. ...
  • Microinjection. ...
  • Transposons/Transposable Elements.

How is genome editing done in plants? ›

The CRISPR–Cas system is an exact and efficient tool for targeted gene editing in plants. This system comprises RNA-guided Cas enzymes, including Cas9, Cpf1, and Cas12a, which recognize specific target sequences within the plant genome and introduce site-specific DNA breaks [29].

Which of the following tools can be used for plant genome editing? ›

Some of the major genome editing tools used to edit plant genomes are: hom*ologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis.

What are the genome editing tools? ›

Advanced genome editing methods engineered from proteins include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and meganucleases. An additional method is called clustered regularly interspaced short palindromic repeats, also known as CRISPR/Cas9.

Can CRISPR be used on plants? ›

CRISPR tools can be used to make changes to plant DNA without adding any foreign DNA. Instead, they can be used to make small edits to the DNA already in plants.

What technology is used to genetically modify plants? ›

Collectively, these techniques are known as recombinant DNA technology. Other terms used for GM plants or foods derived from them are genetically modified organism (GMO), genetically engineered (GE), bioengineered, and transgenic.

What are the disadvantages of genome editing in plants? ›

Critics contend that genome editing can create a range of changes to the genome in plants that pose risks to biodiversity, water and soil, human health, and organic food production. Some are concerned that such crops could outcompete natural species and create broad monocultures, which could wreak havoc on ecosystems.

What is the CRISPR technology for crops? ›

CRISPR-based genome editing is an effective way to improve the nutritional value of crops and render crops safe for people with sensitivities or allergies. It can also be used to combat deficiencies, which is particularly important in vulnerable populations. More sustainable practices.

What is the plant genome editing database? ›

PGED can store information of CRISPR-mediated mutants in any plant species (Fig. 1 and Supplemental Figure S1) and provides a set of tools to facilitate querying, mining and visualizing the stored information. Users begin by choosing the species they are interested in.

What modern tool is now used for genome editing? ›

The CRISPR-Cas9 system consists of two key molecules that introduce a change (mutation) into the DNA. These are: an enzyme called Cas9. This acts as a pair of 'molecular scissors' that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can then be added or removed.

What plants are successful in gene-editing? ›

Currently, CRISPR/Cas9 genome editing has been demonstrated to be successful on a number of influential crops such as maize (Liu et al., 2020; Li et al., 2020b), wheat (Hayta et al., 2019; Liu et al., 2020), and apples (Pompili et al., 2020), with a relatively high transformation efficiency (Haque et al., 2018; ...

What is the new gene-editing tool? ›

CRISPR/Cas9 – a revolutionary gene-editing technology that can be used to modify or correct precise regions of our DNA to treat serious diseases. Dr. Emmanuelle Charpentier, one of our scientific founders, co-invented CRISPR/Cas9 gene editing. She and her collaborator, Dr.

What are the examples of genome editing in plants? ›

[3] Another genome editing tool, TALENs, was used to develop the first genome-edited plant to be commercially grown in the United States and sold as a food product: soybeans that produce high oleic, low linolenic oil that is a healthier alternative to partially hydrogenated oils.

What are genome editing tools in plant breeding? ›

Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas system are the three primary categories of genome-editing tools.

What are the latest genome editing techniques? ›

The core technologies now most commonly used to facilitate genome editing, shown in Figure 1, are (1) clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), (2) transcription activator-like effector nucleases (TALENs), (3) zinc-finger nucleases (ZFNs), and (4) homing ...

What are the 3 main tools in genetic engineering? ›

Tools of genetic engineering include restriction enzymes, DNA ligase, DNA polymerase, and cloning vectors. Restriction enzymes cut DNA at specific recognition sequences, leaving sticky or blunt ends. DNA ligase joins DNA fragments by sealing nicks in DNA strands.

What are the two methods used to genetically modify plants? ›

Traditional methods of modifying plants, like selective breeding and crossbreeding, have been around for nearly 10,000 years. Most of the foods we eat today were originally created using a combination of traditional methods. Two similar plants cross-pollinate to create a new plant.

What machines are used in genetic modification? ›

PCR Machines & Thermal Cyclers

Polymerase Chain Reaction (PCR) machines, also known as thermal cyclers, are indispensable in the genetic engineering lab. They enable the amplification of specific DNA segments, making it possible to work with small samples and conduct detailed analyses.

What are the methods for plant genetic transformation? ›

PGT Methods
  • Electroporation- The electric field creates holes in the plasma membrane, allowing the cell to absorb DNA. ...
  • Biolistic Gene Gun Technique-The term “Particle Bombardment” refers to a biolistic technique of gene transformation in plants.

Top Articles
Latest Posts
Article information

Author: Edmund Hettinger DC

Last Updated:

Views: 6748

Rating: 4.8 / 5 (78 voted)

Reviews: 93% of readers found this page helpful

Author information

Name: Edmund Hettinger DC

Birthday: 1994-08-17

Address: 2033 Gerhold Pine, Port Jocelyn, VA 12101-5654

Phone: +8524399971620

Job: Central Manufacturing Supervisor

Hobby: Jogging, Metalworking, Tai chi, Shopping, Puzzles, Rock climbing, Crocheting

Introduction: My name is Edmund Hettinger DC, I am a adventurous, colorful, gifted, determined, precious, open, colorful person who loves writing and wants to share my knowledge and understanding with you.