Exploring the potential of genome editing CRISPR-Cas9 technology

Gene

Volumn 599, Issue , 2017, Pages 1-18

  Singh, Vijai ^a   Braddick, Darren ^a   Dhar, Pawan Kumar ^b  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

Activation; CRISPR Cas9; CRISPRi; Gene therapy; Genome editing; Indel; Repression; sgRNA

Indexed keywords

ENDONUCLEASE; GUIDE RNA; RNA;

ADAPTIVE IMMUNITY; CRISPR CAS SYSTEM; CRISPR CAS9 SYSTEM; DNA END JOINING REPAIR; DNA REPAIR; DOUBLE STRANDED DNA BREAK; DROSOPHILA; GENE EDITING; GENE LOCUS; GENE TARGETING; GENOME; HEPATITIS B VIRUS; HEPATITIS C VIRUS; HOMOLOGY DIRECTED REPAIR; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN PAPILLOMAVIRUS TYPE 16; HUMAN PAPILLOMAVIRUS TYPE 18; MAMMAL CELL; MEDICAL ETHICS; MICROORGANISM; MOLECULAR IMAGING; NONHUMAN; PRIORITY JOURNAL; REVIEW; SAFETY; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION; ZEBRA; ANIMAL; CHROMOSOMAL MAPPING; ETHICS; GENETIC TRANSCRIPTION; PROCEDURES; TRENDS;

ANIMALS; CHROMOSOME MAPPING; CRISPR-CAS SYSTEMS; GENE EDITING; GENE TARGETING; HUMANS; TRANSCRIPTION, GENETIC;

EID: 84997822099     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2016.11.008     Document Type: Review

References (225)

1. Agari, Y., Sakamoto, K., Tamakoshi, M., Oshima, T., Kuramitsu, S., Shinkai, A., Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J. Mol. Biol. 395 (2010), 270–281.
2. Al-Attar, S., Westra, E.R., van der Oost, J., Brouns, S.J., Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol. Chem. 392:4 (2011), 277–289.
3. Alper, H., Fischer, C., Nevoigt, E., Stephanopoulos, G., Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. U. S. A. 102:36 (2005), 12678–12683.
4. Alper, H., Moxley, J., Nevoigt, E., Fink, G.R., Stephanopoulos, G., Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:5805 (2006), 1565–1568.
5. Amann, R., Fuchs, B.M., Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat. Rev. Microbiol. 6:5 (2008), 339–348.
6. Anantharaman, V., Iyer, L.M., Aravind, L., 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, 2010, 43.
7. 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 5:2 (2014), 163–172.
8. Atkinson, M.R., Savageau, M.A., Myers, J.T., Ninfa, A.J., Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:5 (2003), 597–607.
9. Bachu, R., Bergareche, I., Chasin, L.A., CRISPR-Cas targeted plasmid integration into mammalian cells via non-homologous end joining. Biotechnol. Bioeng. 112:10 (2015), 2154–2162.
10. Bae, S., Park, J., Kim, J.S., Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30:10 (2014), 1473–1475.
11. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 (2007), 1709–1712.
12. Bassett, A.R., Tibbit, C., Ponting, C.P., Liu, J.L., Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4:1 (2013), 220–228.
13. Beisel, C.L., Gomaa, A.A., Barrangou, R., A CRISPR design for next-generation antimicrobials. Genome Biol., 15(11), 2014, 516.
14. Bhaya, D., Davison, M., Barrangou, R., CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 45 (2011), 273–297.
15. Bikard, D., Euler, C.W., Jiang, W., Nussenzweig, P.M., Goldberg, G.W., Duportet, X., et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32:11 (2014), 1146–1150.
16. Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., Marraffini, L.A., Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41:15 (2013), 7429–7437.
17. Blount, K.F., Breaker, R.R., Riboswitches as antibacterial drug targets. Nat. Biotechnol. 24:12 (2006), 1558–1564.
18. Boch, J., TALEs of genome targeting. Nat. Biotechnol. 29:2 (2011), 135–136.
19. Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:5959 (2009), 1509–1512.
20. Briner, A.E., Donohoue, P.D., Gomaa, A.A., Selle, K., Slorach, E.M., Nye, C.H., et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell 56:2 (2014), 333–339.
21. Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Dickman, M.J., et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321 (2008), 960–964.
22. Bugg, T.D., Braddick, D., Dowson, C.G., Roper, D.I., Bacterial cell wall assembly: still an attractive antibacterial target. Trends Biotechnol. 29:4 (2011), 167–173.
23. Carroll, D., Genome engineering with zinc-finger nucleases. Genetics 188:4 (2011), 773–782.
24. Ceol, C.J., Houvras, Y., Jane-Valbuena, J., Bilodeau, S., Orlando, D.A., Battisti, V., et al. The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature 471:7339 (2011), 513–517.
25. Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., et al. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res. 23:4 (2013), 465–472.
26. Chavez, A., Scheiman, J., Vora, S., Pruitt, B.W., Tuttle, M., Iyer, P.R.E., Lin, S., Kiani, S., Guzman, C.D., Wiegand, D.J., Ter-Ovanesyan, D., Braff, J.L., Davidsohn, N., Housden, B.E., Perrimon, N., Weiss, R., Aach, J., Collins, J.J., Church, G.M., Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12:4 (2015), 326–328.
27. Chen, B., Gilbert, L.A., Cimini, B.A., Schnitzbauer, J., Zhang, W., Li, G.W., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:7 (2013), 1479–1491.
28. Chen, H., Choi, J., Bailey, S., Cut site selection by the two nuclease domains of the Cas9 RNA-guided endonuclease. J. Biol. Chem. 289:19 (2014), 13284–13294.
29. Chen, L.C., Yeh, H.Y., Yeh, C.Y., Arias, C.R., Soo, V.W., Identifying co-targets to fight drug resistance based on a random walk model. BMC Syst. Biol., 6, 2012, 5.
30. Chen, Y.Y., Jensen, M.C., Smolke, C.D., Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 8531–8536.
31. Choi, J.G., Dang, Y., Abraham, S., Ma, H., Zhang, J., Guo, H., Cai, Y., Mikkelsen, J.G., Wu, H., Shankar, P., Manjunath, N., Lentivirus pre-packed with Cas9 protein for safer gene editing. Gene Ther. 23:7 (2016), 627–633.
32. Choudhary, E., Thakur, P., Pareek, M., Agarwal, N., Gene silencing by CRISPR interference in mycobacteria. Nat. Commun., 6, 2015, 6267.
33. Chu, V.T., Weber, T., Wefers, B., Wurst, W., Sander, S., Rajewsky, K., et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33:5 (2015), 543–548.
34. Citorik, R.J., Mimee, M., Lu, T.K., Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 32:11 (2014), 1141–1145.
35. Cleto, S., Jensen, J.V., Wendisch, V.F., Lu, T.K., Corynebacterium glutamicum metabolic engineering with CRISPR interference (CRISPRi). ACS Synth. Biol. 5:5 (2016), 375–385.
36. Collins, F., Statement on NIH Funding of Research Using Gene-editing Technologies in Human Embryos. 2015, The NIH Director - National Institutes of Health (NIH), USA.
37. Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339:6121 (2013), 819–823.
38. Cristea, S., Freyvert, Y., Santiago, Y., Holmes, M.C., Urnov, F.D., Gregory, P.D., et al. In vivo cleavage of transgene donors promotes nuclease-mediated targeted integration. Biotechnol. Bioeng. 110 (2013), 871–880.
39. Cui, Y., Li, Y., Gorge, O., Platonov, M.E., Yan, Y., Guo, Z., et al. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS One, 3, 2008, e2652.
40. Culler, S.J., Hoff, K.G., Smolke, C.D., Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330 (2010), 1251–1255.
41. Cyranoski, D., Reardon, S., Chinese scientists genetically modify human embryos. Nat. News, 2015, 10.1038/nature.2015.17378.
42. Danino, T., Mondragón-Palomino, O., Tsimring, L., Hasty, J., A synchronized quorum of genetic clocks. Nature 463:7279 (2010), 326–330.
43. DeBoy, R.T., Mongodin, E.F., Emerson, J.B., Nelson, K.E., Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J. Bacteriol. 188:7 (2006), 2364–2374.
44. Deltcheva, E., Chylinski, K., Sharma, C.M., Gonzales, K., Chao, Y., Pirzada, Z.A., et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471 (2011), 602–607.
45. Deveau, H., Barrangou, R., Garneau, J.E., Labonte, J., Fremaux, C., Boyaval, P., et al. Phage response to CRISPRencoded resistance in Streptococcus thermophilus. J. Bacteriol. 190 (2008), 1390–1400.
46. Deveau, H., Garneau, J.E., Moineau, S., CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 64 (2010), 475–493.
47. DiCarlo, J.E., Norville, J.E., Mali, P., Rios, X., Aach, J., Church, G.M., Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41:7 (2013), 4336–4343.
48. Didovyk, A., Borek, B., Hasty, J., Tsimring, L., Orthogonal modular gene repression in Escherichia coli using engineered CRISPR/Cas9. ACS Synth. Biol. 5:1 (2016), 81–88.
49. Doench, J.G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E.W., Donovan, K.F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., Virgin, H.W., Listgarten, J., Root, D.E., Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34:2 (2016), 184–191.
50. Dominguez, A.A., Lim, W.A., Qi, L.S., Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17:1 (2016), 5–15.
51. Dong, C., Qu, L., Wang, H., Wei, L., Dong, Y., Xiong, S., Targeting hepatitis B virus cccDNA by CRISPR/Cas9 nuclease efficiently inhibits viral replication. Antivir. Res. 118 (2015), 110–117.
52. Dove, S.L., Hochschild, A., Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev. 12 (1998), 745–754.
53. Drummond, I.A., Kidney development and disease in the zebrafish. J. Am. Soc. Nephrol. 16:2 (2005), 299–304.
54. Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 27:8 (2009), 753–759.
55. Ebina, H., Misawa, N., Kanemura, Y., Koyanagi, Y., Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci. Rep., 3, 2013, 2510.
56. Elowitz, M.B., Leibler, S., A synthetic oscillatory network of transcriptional regulators. Nature 403:6767 (2000), 335–338.
57. Endy, D., Foundations for engineering biology. Nature 438:7067 (2005), 449–453.
58. 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 10 (2013), 1116–1121.
59. Fisher, A.L., Ohsako, S., Caudy, M., The WRPW motif of the hairy-related basic helix-loop-helix repressor proteins acts as a 4-amino-acid transcription repression and protein-protein interaction domain. Mol. Cell. Biol. 16:6 (1996), 2670–2677.
60. Friedland, A.E., Baral, R., Singhal, P., Loveluck, K., Shen, S., Sanchez, M., et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol., 16, 2015, 257.
61. Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M., Joung, J.K., Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32:3 (2014), 279–284.
62. Gardner, T.S., Cantor, C.R., Collins, J.J., Construction of a genetic toggle switch in Escherichia coli. Nature 403:6767 (2000), 339–342.
63. Garneau, J.E., Dupuis, M.E., Villion, M., Romero, D.A., Barrangou, R., Boyaval, P., et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468 (2010), 67–71.
64. 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. 109:39 (2012), E2579–E2586.
65. Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., Algire, M.A., et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:5987 (2010), 52–56.
66. Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A. 3rd., Smith, H.O., Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6:5 (2009), 343–345.
67. Gilbert, L.A., Larson, M.H., Morsut, L., Liu, Z., Brar, G.A., Torres, S.E., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:2 (2013), 442–451.
68. Gokcezade, J., Sienski, G., Duchek, P., Efficient CRISPR/Cas9 plasmids for rapid and versatile genome editing in Drosophila. G3 (Bethesda) 4:11 (2014), 2279–2282.
69. Goldshmit, Y., Sztal, T.E., Jusuf, P.R., Hall, T.E., Nguyen-Chi, M., Currie, P.D., Fgf-dependent glial cell bridges facilitate spinal cord regeneration in zebrafish. J. Neurosci. 32:22 (2012), 7477–7492.
70. Gomaa, A.A., Klumpe, H.E., Luo, M.L., Selle, K., Barrangou, R., Beisel, C.L., Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio, 5(1), 2014, 13, e00928.
71. Guan, Y., Ma, Y., Li, Q., Sun, Z., Ma, L., Wu, L., et al. CRISPR/Cas9-mediated somatic correction of a novel coagulator factor IX gene mutation ameliorates hemophilia in mouse. EMBO Mol. Med. 8:5 (2016), 477–488.
72. Hara, S., Tamano, M., Yamashita, S., Kato, T., Saito, T., Sakuma, T., et al. Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Sci. Rep., 5, 2015, 11221.
73. Hathaway, N.A., Bell, O., Hodges, C., Miller, E.L., Neel, D.S., Crabtree, G.R., Dynamics and memory of heterochromatin in living cells. Cell 149:7 (2012), 1447–1460.
74. He, X., Tan, C., Wang, F., Wang, Y., Zhou, R., Cui, D., You, W., Zhao, H., Ren, J., Feng, B., Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair. Nucleic Acids Res., 44(9), 2016, e85.
75. Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., Thakore, P.I., Crawford, G.E., Reddy, T.E., et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33:5 (2015), 510–517.
76. Hisano, Y., Sakuma, T., Nakade, S., Ohga, R., Ota, S., Okamoto, H., et al. Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci. Rep., 5, 2015, 8841.
77. Horlbeck, M.A., Witkowsky, L.B., Guglielmi, B., Replogle, J.M., Gilbert, L.A., Villalta, J.E., Torigoe, S.E., Tjian, R., Weissman, J.S., Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife, 2016, 10.7554/eLife.12677.
78. Horvath, P., Barrangou, R., CRISPR/Cas, the immune system of bacteria and archaea. Science 327:5962 (2010), 167–170.
79. Horvath, P., Romero, D.A., Coûté-Monvoisin, A.C., Richards, M., Deveau, H., Moineau, S., et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190:4 (2008), 1401–1412.
80. Hou, Z., Zhang, Y., Propson, N.E., Howden, S.E., Chu, L.F., Sontheimer, E.J., et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl. Acad. Sci. U. S. A. 110:39 (2013), 15644–15649.
81. Hruscha, A., Krawitz, P., Rechenberg, A., Heinrich, V., Hecht, J., Haass, C., et al. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development 140:24 (2013), 4982–4987.
82. Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31:9 (2013), 827–832.
83. Hu, W., Kaminski, R., Yang, F., Zhang, Y., Cosentino, L., Li, F., et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc. Natl. Acad. Sci. U. S. A. 111:31 (2014), 11461–11466.
84. Huang, H.H., Camsund, D., Lindblad, P., Heidorn, T., Design and characterization of molecular tools for a synthetic biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Res. 38 (2010), 2577–2593.
85. Hutchison, C.A. III, Chuang, R.Y., Noskov, V.N., Assad-Garcia, N., Deerinck, T.J., Ellisman, M.H., et al. Design and synthesis of a minimal bacterial genome. Science, 351(6280), 2016 (aad6253).
86. Hwang, W.Y., Fu, Y., Reyon, D., Maeder, M.L., Tsai, S.Q., Sander, J.D., et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31:3 (2013), 227–229.
87. Isaacs, F.J., Carr, P.A., Wang, H.H., Lajoie, M.J., Sterling, B., Kraal, L., et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333:6040 (2011), 348–353.
88. Isaacs, F.J., Dwyer, D.J., Ding, C., Pervouchine, D.D., Cantor, C.R., Collins, J.J., Engineered riboregulators enable posttranscriptional control of gene expression. Nat. Biotechnol. 22:7 (2004), 841–847.
89. Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., Nakata, A., Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169 (1987), 5429–5433.
90. Jakočiūnas, T., Bonde, I., Herrgård, M., Harrison, S.J., Kristensen, M., Pedersen, L.E., et al. Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab. Eng. 28 (2015), 213–222.
91. Jao, L.E., Wente, S.R., Chen, W., Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. U. S. A. 110:34 (2013), 13904–13909.
92. Jiang, W., Bikard, D., Cox, D., Zhang, F., Marraffini, L.A., RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31:3 (2013), 233–239.
93. Jiang, W., Brueggeman, A.J., Horken, K.M., Plucinak, T.M., Weeks, D.P., Successful transient expression of Cas9 and single guide RNA genes in Chlamydomonas reinhardtii. Eukaryot. Cell 13:11 (2014), 1465–1469.
94. 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 337:6096 (2012), 816–821.
95. Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., Doudna, J., RNA-programmed genome editing in human cells. Elife, 2, 2013, e00471.
96. Kaminski, R., Chen, Y., Fischer, T., Tedaldi, E., Napoli, A., Zhang, Y., et al. Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing. Sci. Rep., 6, 2016, 22555.
97. Kaminski, R., Bella, R., Yin, C., Otte, J., Ferrante, P., Gendelman, H.E., Li, H., Booze, R., Gordon, J., Hu, W., Khalili, K., Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther. 23:8–9 (2016), 690–695.
98. Kemmer, C., Fluri, D.A., Witschi, U., Passeraub, A., Gutzwiller, A., Fussenegger, M., A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. J. Control. Release 150 (2011), 23–29.
99. Kennedy, E.M., Bassit, L.C., Mueller, H., Kornepati, A.V., Bogerd, H.P., et al. Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology 476 (2015), 196–205.
100. Kennedy, E.M., Kornepati, A.V., Goldstein, M., Bogerd, H.P., Poling, B.C., et al. Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease. J. Virol. 88:20 (2014), 11965–11972.
101. Khalil, A.S., Collins, J.J., Synthetic biology: applications come of age. Nat. Rev. Genet. 11:5 (2010), 367–379.
102. Kim, H., Han, H., Ahn, J., Lee, J., Cho, N., Jang, H., et al. Shotgun DNA synthesis for the high throughput construction of large DNA molecules. Nucleic Acids Res., 40, 2012, e140.
103. Kondo, S., Ueda, R., Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics 195:3 (2013), 715–721.
104. Koonin, E.V., Senkevich, T.G., Dolja, V.V., The ancient virus world and evolution of cells. Biol. Direct, 19(1), 2006, 29.
105. Kosuri, S., Eroshenko, N., Leproust, E.M., Super, M., Way, J., Li, J.B., et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat. Biotechnol. 28 (2010), 1295–1299.
106. Lajoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., et al. Genomically recoded organisms expand biological functions. Science 342:6156 (2013), 357–360.
107. Langer-Safer, P.R., Levine, M., Ward, D.C., Immunological method for mapping genes on Drosophila polytene chromosomes. Proc. Natl. Acad. Sci. U. S. A. 79:14 (1982), 4381–4385.
108. Lanphier, E., Urnov, F., Haecker, S.E., Werner, M., Smolenski, J., Don't edit the human germ line. Nature 519 (2015), 410–411.
109. Lartigue, C., Vashee, S., Algire, M.A., Chuang, R.Y., Benders, G.A., Ma, L., et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325 (2009), 1693–1696.
110. Lawhorn, I.E., Ferreira, J.P., Wang, C.L., Evaluation of sgRNA target sites for CRISPR-mediated repression of TP53. PLoS One, 9(11), 2014, e113232.
111. Lee, J.S., Kallehauge, T.B., Pedersen, L.E., Kildegaard, H.F., Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Sci. Rep., 5, 2015, 8572.
112. Li, C., Guan, X., Du, T., Jin, W., Wu, B., Liu, Y., et al. Inhibition of HIV-1 infection of primary CD4 + T cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J. Gen. Virol. 96:8 (2015), 2381–2393.
113. Liang, X., Potter, J., Kumar, S., Zou, Y., Quintanilla, R., Sridharan, M., et al. Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. J. Biotechnol. 208 (2015), 44–53.
114. Liang, P., Xu, Y., Zhang, X., Ding, C., Huang, R., Zhang, Z., Lv, J., Xie, X., Chen, Y., Li, Y., Sun, Y., Bai, Y., Songyang, Z., Ma, W., Zhou, C., Huang, J., CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 6:5 (2015), 363–372.
115. Liao, J., Karnik, R., Gu, H., Ziller, M.J., Clement, K., Tsankov, A.M., et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stemcells. Nat. Genet. 47:5 (2015), 469–478.
116. Liao, H.K., Gu, Y., Diaz, A., Marlett, J., Takahashi, Y., Li, M., et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat. Commun., 6, 2015, 6413.
117. Lin, S.R., Yang, H.C., Kuo, Y.T., Liu, C.J., Yang, T.Y., Sung, K.C., et al. The CRISPR/Cas9 system facilitates clearance of the intrahepatic HBV templates in vivo. Mol. Ther. Nucleic Acids, 3, 2014, e186.
118. Lindblad, P., Lindberg, P., Oliveira, P., Stensjö, K., Heidorn, T., Design, engineering, and construction of photosynthetic microbial cell factories for renewable solar fuel production. Ambio 41:2 (2012), 163–168.
119. Liu, H., Wei, Z., Dominguez, A., Li, Y., Wang, X., Qi, L.S., CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 31:22 (2015), 3676–3678.
120. Liu, Y.C., Cai, Z.M., Zhang, X.J., Reprogrammed CRISPR-Cas9 targeting the conserved regions of HPV6/11 E7 genes inhibits proliferation and induces apoptosis in E7-transformed keratinocytes. Asian J. Androl. 18:3 (2016), 475–479.
121. Long, C., McAnally, J.R., Shelton, J.M., Mireault, A.A., Bassel-Duby, R., Olson, E.N., Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA. Science 345:6201 (2014), 1184–1188.
122. Long, C., Amoasii, L., Mireault, A.A., McAnally, J.R., Li, H., Sanchez-Ortiz, E., Bhattacharyya, S., Shelton, J.M., Bassel-Duby, R., Olson, E.N., Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351:6271 (2016), 400–403.
123. Ma, H., Naseri, A., Reyes-Gutierrez, P., Wolfe, S.A., Zhang, S., Pederson, T., Multicolor CRISPR labeling of chromosomal loci in human cells. Proc. Natl. Acad. Sci. U. S. A. 112:10 (2015), 3002–3007.
124. 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. Methods 10:10 (2013), 977–979.
125. Makarova, K.S., Aravind, L., Grishin, N.V., Rogozin, I.B., Koonin, E.V., A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30 (2002), 482–496.
126. Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., et al. RNA-guided human genome engineering via Cas9. Science 339:6121 (2013), 823–826.
127. Manco-Johnson, M.J., Abshire, T.C., Shapiro, A.D., Riske, B., Hacker, M.R., Kilcoyne, R., et al. Prophylaxis versus episodic treatment to prevent joint disease in boys with severe hemophilia. N. Engl. J. Med. 357:6 (2007), 535–544.
128. Mandegar, M.A., Huebsch, N., Frolov, E.B., Shin, E., Truong, A., Olvera, M.P., Chan, A.H., Miyaoka, Y., Holmes, K., Spencer, C.I., Judge, L.M., Gordon, D.E., Eskildsen, T.V., Villalta, J.E., Horlbeck, M.A., Gilbert, L.A., Krogan, N.J., Sheikh, S.P., Weissman, J.S., Qi, L.S., So, P.L., Conklin, B.R., CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs. Cell Stem Cell 18:4 (2016), 541–553.
129. 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. 23 (2013), 539–546.
130. Margolin, J.F., Friedman, J.R., Meyer, W.K., Vissing, H., Thiesen, H.J., Rauscher, F.J. 3rd., Krüppel-associated boxes are potent transcriptional repression domains. Proc. Natl. Acad. Sci. U. S. A. 91:10 (1994), 4509–4513.
131. Marraffini, L.A., Sontheimer, E.J., CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322 (2008), 1843–1845.
132. Maruyama, T., Dougan, S.K., Truttmann, M.C., Bilate, A.M., Ingram, J.R., Ploegh, H.L., Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 33:5 (2015), 538–542.
133. Mashimo, T., Gene targeting technologies in rats: zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats. Develop. Growth Differ. 56:1 (2014), 46–52.
134. Ménoret, S., De Cian, A., Tesson, L., Remy, S., Usal, C., Boulé, J.B., Boix, C., Fontanière, S., Crénéguy, A., Nguyen, T.H., Brusselle, L., Thinard, R., Gauguier, D., Concordet, J.P., Cherifi, Y., Fraichard, A., Giovannangeli, C., Anegon, I., Homology-directed repair in rodent zygotes using Cas9 and TALEN engineered proteins. Sci. Rep., 5, 2015, 14410.
135. Millen, A.M., Horvath, P., Boyaval, P., Romero, D.A., Mobile CRISPR/Cas-mediated bacteriophage resistance in Lactococcus lactis. PLoS One, 7(12), 2012, e51663.
136. Mojica, F.J., Díez-Villaseñor, C., García-Martínez, J., Almendros, C., Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155:3 (2009), 733–740.
137. Mojica, F.J., Ferrer, C., Juez, G., Rodriguez-Valera, F., Long stretches of short tandem repeats are present in the largest replicons of the archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 17 (1995), 85–93.
138. Moon, T.S., Lou, C., Tamsir, A., Stanton, B.C., Voigt, C.A., Genetic programs constructed from layered logic gates in single cells. Nature 491:7423 (2012), 249–253.
139. Moscou, M.J., Bogdanove, A.J., A simple cipher governs DNA recognition by TAL effectors. Science, 326(5959), 2009, 1501.
140. Na, D., Yoo, S.M., Chung, H., Park, H., Park, J.H., Lee, S.Y., Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. Biotechnol. 31:2 (2013), 170–174.
141. Naito, Y., Hino, K., Bono, H., Ui-Tei, K., CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31:7 (2015), 1120–1123.
142. Nelson, C.E., Hakim, C.H., Ousterout, D.G., Thakore, P.I., Moreb, E.A., Castellanos Rivera, R.M., et al. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351:6271 (2016), 403–407.
143. Nielsen, A.A., Voigt, C.A., Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol. Syst. Biol., 10, 2014, 763.
144. Nissim, L., Bar-Ziv, R.H., A tunable dual-promoter integrator for targeting of cancer cells. Mol. Syst. Biol., 6, 2010, 444.
145. Nordmann, P., Dortet, L., Poirel, L., Carbapenem resistance in Enterobacteriaceae: here is the storm!. Trends Mol. Med. 18 (2012), 263–272.
146. Ota, S., Hisano, Y., Ikawa, Y., Kawahara, A., Multiple genome modifications by the CRISPR/Cas9 system in zebrafish. Genes Cells 19:7 (2014), 555–564.
147. Otieno, M.O., CRISPR-Cas9 human genome editing: challenges, ethical concerns and implications. J. Clin. Res. Bioethics, 6, 2015, 253.
148. Pabo, C.O., Peisach, E., Grant, R.A., Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 70 (2001), 313–340.
149. Park, J., Bae, S., Kim, J.S., Cas-designer: a web-based tool for choice of CRISPR-Cas9 target sites. Bioinformatics 31:24 (2015), 4014–4016.
150. Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Polstein, L.R., et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10:10 (2013), 973–976.
151. Pfleger, B.F., Pitera, D.J., Smolke, C.D., Keasling, J.D., Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 24:8 (2006), 1027–1032.
152. Platt, R.J., Chen, S., Zhou, Y., Yim, M.J., Swiech, L., Kempton, H.R., et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159:2 (2014), 440–455.
153. Polstein, L.R., Gersbach, C.A., A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 11:3 (2015), 198–200.
154. Port, F., Chen, H.M., Lee, T., Bullock, S.L., Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc. Natl. Acad. Sci. U. S. A. 111:29 (2014), E2967–E2976.
155. Price, A.A., Sampson, T.R., Ratner, H.K., Grakoui, A., Weiss, D.S., Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc. Natl. Acad. Sci. U. S. A. 112:19 (2015), 6164–6169.
156. Purnick, P.E., Weiss, R., The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10:6 (2009), 410–422.
157. Pyne, M.E., Moo-Young, M., Chung, D.A., Chou, C.P., Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl. Environ. Microbiol. 81:15 (2015), 5103–5114.
158. Qi, L.S., Arkin, A.P., A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat. Rev. Microbiol. 12:5 (2014), 341–354.
159. Qi, L.S., Larson, M.H., Gilbert, L.A., Doudna, J.A., Weissman, J.S., Arkin, A.P., et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:5 (2013), 1173–1183.
160. Ran, F.A., Cong, L., Yan, W.X., Scott, D.A., Gootenberg, J.S., Kriz, A.J., et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520 (2015), 186–191.
161. Ranganathan, V., Wahlin, K., Maruotti, J., Zack, D.J., Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs. Nat. Commun., 5, 2014, 4516.
162. Rees, D.C., Williams, T.N., Gladwin, M.T., Sickle-cell disease. Lancet 376:9757 (2010), 2018–2031.
163. Reiter, L.T., Potocki, L., Chien, S., Gribskov, M., Bier, E., A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res. 11:6 (2001), 1114–1125.
164. Ren, X., Sun, J., Housden, B.E., Hu, Y., Roesel, C., Lin, S., et al. Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc. Natl. Acad. Sci. U. S. A. 110:47 (2013), 19012–19017.
165. Ren, X., Yang, Z., Mao, D., Chang, Z., Qiao, H.H., Wang, X., et al. Performance of the Cas9 nickase system in Drosophila melanogaster. G3 (Bethesda) 4:10 (2014), 1955–1962.
166. Ren, X., Yang, Z., Xu, J., Sun, J., Mao, D., Hu, Y., et al. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep. 9:3 (2014), 1151–1162.
167. Richter, C., Chang, J.T., Fineran, P.C., Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. Viruses 4:10 (2012), 2291–2311.
168. Riehle, M.M., Bennett, A.F., Long, A.D., Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 98:2 (2001), 525–530.
169. Robertson, K.D., DNA methylation and human disease. Nat. Rev. Genet. 6:8 (2005), 597–610.
170. Ronda, C., Pedersen, L.E., Sommer, M.O., Nielsen, A.T., CRMAGE: CRISPR optimized MAGE recombineering. Sci. Rep., 6, 2016, 19452.
171. Rovner, A.J., Haimovich, A.D., Katz, S.R., Li, Z., Grome, M.W., Gassaway, B.M., et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 518:7537 (2015), 89–93.
172. Saayman, S., Ali, S.A., Morris, K.V., Weinberg, M.S., The therapeutic application of CRISPR/Cas9 technologies for HIV. Expert. Opin. Biol. Ther. 15:6 (2015), 819–830.
173. Saayman, S.M., Lazar, D.C., Scott, T.A., Hart, J.R., Takahashi, M., Burnett, J.C., Planelles, V., Morris, K.V., Weinberg, M.S., Potent and targeted activation of latent HIV-1 using the CRISPR/dCas9 activator complex. Mol. Ther. 24:3 (2016), 488–498.
174. Sakuma, T., Takenaga, M., Kawabe, Y., Nakamura, T., Kamihira, M., Yamamoto, T., Homologous recombination-independent large gene cassette knock-in in CHO cells using TALEN and MMEJ-directed donor plasmids. Int. J. Mol. Sci. 16:10 (2015), 23849–23866.
175. Salis, H.M., Mirsky, E.A., Voigt, C.A., Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27:10 (2009), 946–950.
176. 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. 39:21 (2011), 9275–9282.
177. Schiffman, M., Castle, P.E., Jeronimo, J., Rodriguez, A.C., Wacholder, S., Human papillomavirus and cervical cancer. Lancet 370:9590 (2007), 890–907.
178. Selle, K., Barrangou, R., Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol. 23:4 (2015), 225–232.
179. Shis, D.L., Bennett, M.R., Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc. Natl. Acad. Sci. U. S. A. 110:13 (2013), 5028–5033.
180. Singh, V., Recent advancements in synthetic biology: current status and challenges. Gene 535:1 (2014), 1–11.
181. Singh, V., Recent advances and opportunities in synthetic logic gates engineering in living cells. Syst. Synth. Biol. 8:4 (2014), 271–282.
182. Singh, V., Chaudhary, D.K., Mani, I., Dhar, P.K., Recent advances and challenges of the use of cyanobacteria towards the production of biofuels. Renew. Sust. Energ. Rev. 60 (2016), 1–10.
183. Singh, V., Mani, I., Chaudhary, D.K., Somvanshi, P., The β-Ketoacyl-ACP synthase from Mycobacterium tuberculosis as potential drugs target. Curr. Med. Chem. 18:9 (2011), 1318–1324.
184. Singh, V., Somvanshi, P., Homology modeling of 3-oxoacyl-acyl carrier protein synthase II (KAS II) from Mycobacterium tuberculosis H37Rv and molecular docking for exploration of drugs. J. Mol. Model. 15:5 (2009), 453–460.
185. Singh, V., Somvanshi, P., Toward the virtual screening of potential drugs in the homology modeled NAD + dependent DNA ligase from Mycobacterium tuberculosis. Protein Pept. Lett. 17:2 (2010), 269–276.
186. 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. 30 (2011), 1335–1342.
187. Smith, I., Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin. Microbiol. Rev. 16:3 (2003), 463–496.
188. Smith, P.A., Romesberg, F.E., Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nat. Chem. Biol. 3:9 (2007), 549–556.
189. Soma, Y., Tsuruno, K., Wada, M., Yokota, A., Hanai, T., Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab. Eng. 23 (2014), 175–184.
190. Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J., Mateo, J.L., CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One, 10(4), 2015, e0124633.
191. Stricker, J., Cookson, S., Bennett, M.R., Mather, W.H., Tsimring, L.S., Hasty, J., A fast, robust and tunable synthetic gene oscillator. Nature 456:7221 (2008), 516–519.
192. Szczepankowska, A., Role of CRISPR/cas system in the development of bacteriophage resistance. Adv. Virus Res. 82 (2012), 289–338.
193. Szczepek, M., Brondani, V., Büchel, J., Serrano, L., Segal, D.J., Cathomen, T., Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat. Biotechnol. 25:7 (2007), 786–793.
194. Tabebordbar, M., Zhu, K., Cheng, J.K., Chew, W.L., Widrick, J.J., Yan, W.X., Maesner, C., Wu, E.Y., Xiao, R., Ran, F.A., Cong, L., Zhang, F., Vandenberghe, L.H., Church, G.M., Wagers, A.J., In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351:6271 (2016), 407–411.
195. Tamsir, A., Tabor, J.J., Voigt, C.A., Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469 (2011), 212–215.
196. Tanenbaum, M.E., Gilbert, L.A., Qi, L.S., Weissman, J.S., Vale, R.D., A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:3 (2014), 635–646.
197. Thakore, P.I., D'Ippolito, A.M., Song, L., Safi, A., Shivakumar, N.K., Kabadi, A.M., et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12:12 (2015), 1143–1149.
198. Thomas, C.E., Ehrhardt, A., Kay, M.A., Progress and problems with the use of viral vectors for gene therapy. Nat. Rev. Genet. 4 (2003), 346–358.
199. Tong, Y., Charusanti, P., Zhang, L., Weber, T., Lee, S.Y., CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth. Biol. 4:9 (2015), 1020–1029.
200. Tucker, B.J., Breaker, R.R., Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15:3 (2005), 342–348.
201. Wang, H.H., Huang, P.Y., Xu, G., Haas, W., Marblestone, A., Li, J., et al. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth. Biol. 1:2 (2012), 43–52.
202. Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R., et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:7257 (2009), 894–898.
203. Wang, J., Quake, S.R., RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection. Proc. Natl. Acad. Sci. U. S. A. 111:36 (2014), 13157–13162.
204. Wang, W., Ye, C., Liu, J., Zhang, D., Kimata, J.T., Zhou, P., CCR5 gene disruption via lentiviral vectors expressing Cas9 and single guided RNA renders cells resistant to HIV-1 infection. PLoS One, 9(12), 2014, e115987.
205. Wang, Z., Pan, Q., Gendron, P., Zhu, W., Guo, F., Cen, S., Wainberg, M.A., Liang, C., CRISPR/Cas9-derived mutations both inhibit HIV-1 replication and accelerate viral escape. Cell Rep. 15:3 (2016), 481–489.
206. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., et al. The sequence of the human genome. Science 291:5507 (2001), 1304–1351.
207. White, M.K., Hu, W., Khalili, K., The CRISPR/Cas9 genome editing methodology as a weapon against human viruses. Discov. Med. 19:105 (2015), 255–262.
208. Win, M.N., Smolke, C.D., Higher-order cellular information processing with synthetic RNA devices. Science 322:5900 (2008), 456–460.
209. Wu, H., Wang, Y., Wang, Y., Cao, X., Wu, Y., Meng, Z., et al. Quantitatively relating gene expression to light intensity via the serial connection of blue light sensor and CRISPRi. ACS Synth. Biol. 3:12 (2014), 979–982.
210. Wurm, F.M., Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 22:11 (2004), 1393–1398.
211. Xue, Z., Wu, M., Wen, K., Ren, M., Long, L., Zhang, X., et al. CRISPR/Cas9 mediates efficient conditional mutagenesis in Drosophila. G3 (Bethesda) 4:11 (2014), 2167–2173.
212. Yao, L., Cengic, I., Anfelt, J., Hudson, E.P., Multiple gene repression in cyanobacteria using CRISPRi. ACS Synth. Biol. 5:3 (2016), 207–212.
213. Ye, L., Wang, J., Beyer, A.I., Teque, F., Cradick, T.J., Qi, Z., et al. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection. Proc. Natl. Acad. Sci. U. S. A. 111:26 (2014), 9591–9596.
214. Yim, E.K., Park, J.S., The role of HPV E6 and E7 oncoproteins in HPV-associated cervical carcinogenesis. Cancer Res. Treat. 37:6 (2005), 319–324.
215. Yin, H., Xue, W., Chen, S., Bogorad, R.L., Benedetti, E., Grompe, M., et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32:6 (2014), 551–553.
216. Yin, H., Kanasty, R.L., Eltoukhy, A.A., Vegas, A.J., Dorkin, J.R., Anderson, D.G., Non-viral vectors for gene-based therapy. Nat. Rev. Genet. 15 (2014), 541–555.
217. Yin, C., Zhang, T., Li, F., Yang, F., Putatunda, R., Young, W.B., Khalili, K., Hu, W., Zhang, Y., Functional screening of guide RNAs targeting the regulatory and structural HIV-1 viral genome for a cure of AIDS. AIDS 30:8 (2016), 1163–1174.
218. Young, R.F. 3rd., Molecular biology. Secret weapon. Science 321:5891 (2008), 922–923.
219. Yuen, K.S., Chan, C.P., Wong, N.H., Ho, C.H., Ho, T.H., Lei, T., et al. CRISPR/Cas9-mediated genome editing of Epstein-Barr virus in human cells. J. Gen. Virol. 96 (2015), 626–636.
220. Zalatan, J.G., Lee, M.E., Almeida, R., Gilbert, L.A., Whitehead, E.H., La Russa, M., et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160 (2015), 339–350.
221. Zeng, Z., Human genes involved in hepatitis B virus infection. World J. Gastroenterol. 20:24 (2014), 7696–7706.
222. Zhang, R., Miner, J.J., Gorman, M.J., Rausch, K., Ramage, H., White, J.P., Zuiani, A., Zhang, P., Fernandez, E., Zhang, Q., Dowd, K.A., Pierson, T.C., Cherry, S., Diamond, M.S., A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 535:7610 (2016), 164–168.
223. Zhang, Z., Chen, C., Li, Z., Wu, Y.H., Xiao, X.M., Individualized management of pregnant women with high hepatitis B virus DNA levels. World J. Gastroenterol. 20:34 (2014), 12056–12061.
224. Zhen, S., Hua, L., Liu, Y.H., Gao, L.C., Fu, J., Wan, D.Y., et al. Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Gene Ther. 22:5 (2015), 404–412.
225. Zhu, W., Lei, R., Le Duff, Y., Li, J., Guo, F., Wainberg, M.A., et al. The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA. Retrovirology, 12, 2015, 22.