Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

Current Opinion in Plant Biology

Volumn 30, Issue , 2016, Pages 70-77

  Liu, Degao ^a   Hu, Rongbin ^a   Palla, Kaitlin J ^a   Tuskan, Gerald A ^a   Yang, Xiaohan ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENETIC ENGINEERING; GENETICS; GENOMICS; PLANT GENOME; PROCEDURES; TRANSGENIC PLANT;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; GENETIC ENGINEERING; GENOME, PLANT; GENOMICS; MODELS, BIOLOGICAL; PLANTS, GENETICALLY MODIFIED;

EID: 84958241188     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2016.01.007     Document Type: Review

References (73)

1. Whitham T.G., Young W.P., Martinsen G.D., Gehring C.A., Schweitzer J.A., Shuster S.M., Wimp G.M., Fischer D.G., Bailey J.K., Lindroth R.L., et al. Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 2003, 84:559-573.
2. Weston D.J., Rogers A., Tschaplinski T.J., Gunter L.E., Jawdy S.A., Engle N.L., Heady L.E., Tuskan G.A., Wullschleger S.D. Scaling nitrogen and carbon interactions: what are the consequences of biological buffering?. Ecol Evol 2015, 5:2839-2850.
3. Jansson C., Wullschleger S.D., Kalluri U.C., Tuskan G.A. Phytosequestration: carbon biosequestration by plants and the prospects of genetic engineering. Bioscience 2010, 60:685-696.
4. Lamit L.J., Lau M.K., Næsborg R.R., Wojtowicz T., Whitham T.G., Gehring C.A. Genotype variation in bark texture drives lichen community assembly across multiple environments. Ecology 2015, 96:960-971.
5. Yang X., Cushman J.C., Borland A.M., Edwards E.J., Wullschleger S.D., Tuskan G.A., Owen N.A., Griffiths H., Smith J.A.C., De Paoli H.C., et al. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 2015, 207:491-504.
6. Ragauskas A.J., Beckham G.T., Biddy M.J., Chandra R., Chen F., Davis M.F., Davison B.H., Dixon R.A., Gilna P., Keller M., et al. Lignin valorization: improving lignin processing in the biorefinery. Science 2014, 344:1246843.
7. Tuskan G. Short-rotation woody crop supply systems in the United States: what do we know and what do we need to know?. Biomass Bioenergy 1998, 14:307-315.
8. Harfouche A., Meilan R., Kirst M., Morgante M., Boerjan W., Sabatti M., Mugnozza G.S. Accelerating the domestication of forest trees in a changing world. Trends Plant Sci 2012, 17:64-72.
9. Alonso J.M., Stepanova A.N., Leisse T.J., Kim C.J., Chen H., Shinn P., Stevenson D.K., Zimmerman J., Barajas P., Cheuk R., et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 2003, 301:653-657.
10. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
11. Weigel D., Ahn J.H., Blázquez M.A., Borevitz J.O., Christensen S.K., Fankhauser C., Ferrándiz C., Kardailsky I., Malancharuvil E.J., Neff M.M., et al. Activation tagging in Arabidopsis. Plant Physiol 2000, 122:1003-1014.
12. Belhaj K., Chaparro-Garcia A., Kamoun S., Patron N.J., Nekrasov V. Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 2015, 32:76-84.
13. 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.
14. Xu P., Zhang Y., Kang L., Roossinck M.J., Mysore K.S. Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol 2006, 142:429-440.
15. Shalem O., Sanjana N.E., Zhang F. High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet 2015, 16:299-311.
16. Barrangou R., Birmingham A., Wiemann S., Beijersbergen R.L., Hornung V., van Brabant Smith A. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res 2015, gkv226.
17. Bortesi L., Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 2015, 33:41-52.
18. Belhaj K., Chaparro-Garcia A., Kamoun S., Nekrasov V. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 2013, 9:39.
19. Schaeffer S.M., Nakata P.A. CRISPR/Cas9-mediated genome editing and gene replacement in plants: transitioning from lab to field. Plant Sci 2015.
20. Zhou X., Jacobs T.B., Xue L.J., Harding S.A., Tsai C.J. Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate: CoA ligase specificity and redundancy. New Phytol 2015, 208:298-301.
21. Fan D., Liu T., Li C., Jiao B., Li S., Hou Y., Luo K. Efficient CRISPR/Cas9-mediated targeted mutagenesis in Populus in the first generation. Sci Rep 2015, 5:12217.
22. Jain M. Functional genomics of abiotic stress tolerance in plants: a CRISPR approach. Front Plant Sci 2015, 6:375.
23. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604.
24. Myburg A.A., Grattapaglia D., Tuskan G.A., Hellsten U., Hayes R.D., Grimwood J., Jenkins J., Lindquist E., Tice H., Bauer D., et al. The genome of Eucalyptus grandis. Nature 2014, 510:356-362.
25. Xie K., Minkenberg B., Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci U S A 2015, 112:3570-3575.
26. 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.
27. Li J.-F., Norville J.E., Aach J., McCormack M., Zhang D., Bush J., Church G.M., Sheen J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 2013, 31:688-691.
28. Schiml S., Fauser F., Puchta H. The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J 2014, 80:1139-1150.
29. Baltes N.J., Gil-Humanes J., Cermak T., Atkins P.A., Voytas D.F. DNA replicons for plant genome engineering. Plant Cell 2014, 26:151-163.
30. Čermák T., Baltes N.J., Čegan R., Zhang Y., Voytas D.F. High-frequency, precise modification of the tomato genome. Genome Biol 2015, 16:1-15.
31. Firoozabady E., DeBoer D.L., Merlo D.J., Halk E.L., Amerson L.N., Rashka K.E., Murray E.E. Transformation of cotton (Gossypium hirsutum L.) by Agrobacterium tumefaciens and regeneration of transgenic plants. Plant Mol Biol 1987, 10:105-116.
32. Cseke L.J., Cseke S.B., Podila G.K. High efficiency poplar transformation. Plant Cell Rep 2007, 26:1529-1538.
33. Yu B., Zhai H., Wang Y., Zang N., He S., Liu Q. Efficient Agrobacterium tumefaciens-mediated transformation using embryogenic suspension cultures in sweetpotato, Ipomoea batatas (L.) Lam. Plant Cell Tiss Org 2007, 90:265-273.
34. Wang Y., Cheng X., Shan Q., Zhang Y., Liu J., Gao C., Qiu J.-L. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 2014, 32:947-951.
35. Maresca M., Lin V.G., Guo N., Yang Y. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res 2013, 23:539-546.
36. Nandy S., Srivastava V. Marker-free site-specific gene integration in rice based on the use of two recombination systems. Plant Biotechnol J 2012, 10:904-912.
37. Woo J.W., Kim J., Kwon S.I., Corvalán C., Cho S.W., Kim H., Kim S.-G., Kim S.-T., Choe S., Kim J.-S. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol 2015.
38. Vardi A., Bleichman S., Aviv D. Genetic transformation of Citrus protoplasts and regeneration of transgenic plants. Plant Sci 1990, 69:199-206.
39. Maddumage R., Fung R.M., Weir I., Ding H., Simons J.L., Allan A.C. Efficient transient transformation of suspension culture-derived apple protoplasts. Plant Cell Tiss Org 2002, 70:77-82.
40. Ragauskas A.J., Williams C.K., Davison B.H., Britovsek G., Cairney J., Eckert C.A., Frederick W.J., Hallett J.P., Leak D.J., Liotta C.L., et al. The path forward for biofuels and biomaterials. Science 2006, 311:484-489.
41. Sander J.D., Joung J.K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014, 32:347-355.
42. 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.
43. 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.
44. Nihongaki Y., Kawano F., Nakajima T., Sato M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat Biotechnol 2015, 33:755-760.
45. Polstein L.R., Gersbach C.A. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol 2015, 11:198-200.
46. Nihongaki Y., Yamamoto S., Kawano F., Suzuki H., Sato M. CRISPR-Cas9-based photoactivatable transcription system. Chem Biol 2015, 22:169-174.
47. Zetsche B., Volz S.E., Zhang F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat Biotechnol 2015, 33:139-142.
48. Dow L.E., Fisher J., O'Rourke K.P., Muley A., Kastenhuber E.R., Livshits G., Tschaharganeh D.F., Socci N.D., Lowe S.W. Inducible in vivo genome editing with CRISPR-Cas9. Nat Biotechnol 2015, 33:390-394.
49. Ablain J., Durand E.M., Yang S., Zhou Y., Zon L.I. A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. Dev Cell 2015, 32:756-764.
50. Shechner D.M., Hacisuleyman E., Younger S.T., Rinn J.L. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods 2015, 12:664-670.
51. Deng W., Shi X., Tjian R., Lionnet T., Singer R.H. CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci U S A 2015, 112:11870-11875.
52. Chen B., Gilbert L.A., Cimini B.A., Schnitzbauer J., Zhang W., Li G.-W., Park J., Blackburn E.H., Weissman J.S., Qi L.S., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013, 155:1479-1491.
53. Robson P., Jensen E., Hawkins S., White S.R., Kenobi K., Clifton-Brown J., Donnison I., Farrar K. Accelerating the domestication of a bioenergy crop: identifying and modelling morphological targets for sustainable yield increase in Miscanthus. J Exp Bot 2013, 64:4143-4155.
54. Tornow S., Mewes H. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res 2003, 31:6283-6289.
55. Wang X., Dalkic E., Wu M., Chan C. Gene module level analysis: identification to networks and dynamics. Curr Opin Biotechnol 2008, 19:482-491.
56. Wang T., Wei J.J., Sabatini D.M., Lander E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014, 343:80-84.
57. Koike-Yusa H., Li Y., Tan E.-P., Velasco-Herrera M.D.C., Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 2014, 32:267-273.
58. Parnas O., Jovanovic M., Eisenhaure T.M., Herbst R.H., Dixit A., Ye C.J., Przybylski D., Platt R.J., Tirosh I., Sanjana N.E., et al. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 2015, 162:675-686.
59. Bassett A.R., Kong L., Liu J.L. A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells. J Genet Genomics 2015, 42:301-309.
60. Takken F.L., Luderer R., Gabriëls S.H., Westerink N., Lu R., De Wit P.J., Joosten M.H. A functional cloning strategy, based on a binary PVX-expression vector, to isolate HR-inducing cDNAs of plant pathogens. Plant J 2000, 24:275-283.
61. Karrer E.E., Beachy R.N., Holt C.A. Cloning of tobacco genes that elicit the hypersensitive response. Plant Mol Biol 1998, 36:681-690.
62. Heckl D., Kowalczyk M.S., Yudovich D., Belizaire R., Puram R.V., McConkey M.E., Thielke A., Aster J.C., Regev A., Ebert B.L. Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing. Nat Biotechnol 2014, 32:941-946.
63. Lowder L.G., Paul J.W., Baltes N.J., Voytas D.F., Zhang Y., Zhang D., Tang X., Zheng X., Hsieh T.-F., Qi Y. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 2015, 169:971-985.
64. Xing H.L., Dong L., Wang Z.P., Zhang H.Y., Han C.Y., Liu B., Wang X.C., Chen Q.J. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 2014, 14:327.
65. De Paoli H.C., Tuskan G.A., Yang X. An innovative platform for quick and flexible joining of assorted DNA fragments. Sci Rep-UK 2016, 6:19278.
66. Ainley W.M., Sastry-Dent L., Welter M.E., Murray M.G., Zeitler B., Amora R., Corbin D.R., Miles R.R., Arnold N.L., Strange T.L., et al. Trait stacking via targeted genome editing. Plant Biotechnol J 2013, 11:1126-1134.
67. Kumar S., AlAbed D., Worden A., Novak S., Wu H., Ausmus C., Beck M., Robinson H., Minnicks T., Hemingway D., et al. A modular gene targeting system for sequential transgene stacking in plants. J Biotechnol 2015, 207:12-20.
68. D'Halluin K., Vanderstraeten C., Hulle J., Rosolowska J., Den Brande I., Pennewaert A., D'Hont K., Bossut M., Jantz D., Ruiter R., et al. Targeted molecular trait stacking in cotton through targeted double-strand break induction. Plant Biotechnol J 2013, 11:933-941.
69. Zalatan J.G., Lee M.E., Almeida R., Gilbert L.A., Whitehead E.H., La Russa M., Tsai J.C., Weissman J.S., Dueber J.E., Qi L.S., et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 2015, 160:339-350.
70. Mimee M., Tucker A.C., Voigt C.A., Lu T.K. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Systems 2015, 1:62-71.
71. Li Y., Jiang Y., Chen H., Liao W., Li Z., Weiss R., Xie Z. Modular construction of mammalian gene circuits using TALE transcriptional repressors. Nat Chem Biol 2015, 11:207-213.
72. Hu W.-J., Kawaoka A., Tsai C.-J., Lung J., Osakabe K., Ebinuma H., Chiang V.L. Compartmentalized expression of two structurally and functionally distinct 4-coumarate: CoA ligase genes in aspen (Populus tremuloides). Proc Natl Acad Sci U S A 1998, 95:5407-5412.
73. Harding S.A., Leshkevich J., Chiang V.L., Tsai C.-J. Differential substrate inhibition couples kinetically distinct 4-coumarate: coenzyme A ligases with spatially distinct metabolic roles in quaking aspen. Plant Physiol 2002, 128:428-438.