Open Access
Issue
E3S Web Conf.
Volume 233, 2021
2020 2nd International Academic Exchange Conference on Science and Technology Innovation (IAECST 2020)
Article Number 02004
Number of page(s) 9
Section BFS2020-Biotechnology and Food Science
DOI https://doi.org/10.1051/e3sconf/202123302004
Published online 27 January 2021
  1. Doudna, J. A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096, doi:10.1126/science.1258096 (2014). [Google Scholar]
  2. Li, H. et al. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther 5, 1, doi:10.1038/s41392-019-0089-y (2020). [CrossRef] [PubMed] [Google Scholar]
  3. Rudin, N., Sugarman, E. & Haber, J. E. Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. Genetics 122, 519-534 (1989). [CrossRef] [PubMed] [Google Scholar]
  4. Cannan, W. J. & Pederson, D. S. Mechanisms and Consequences of Double-Strand DNA Break Formation in Chromatin. J Cell Physiol 231, 3-14, doi:10.1002/jcp.25048 (2016). [Google Scholar]
  5. Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278, doi:10.1016/j.cell.2014.05.010 (2014). [CrossRef] [PubMed] [Google Scholar]
  6. Bibikova, M. et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21, 289-297, doi:10.1128/MCB.21.1.289-297.2001 (2001). [CrossRef] [PubMed] [Google Scholar]
  7. Haber, J. E. A Life Investigating Pathways That Repair Broken Chromosomes. Annu Rev Genet 50, 1-28, doi:10.1146/annurev-genet-120215-035043 (2016). [CrossRef] [PubMed] [Google Scholar]
  8. Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat Cell Biol 21, 1468-1478, doi:10.1038/s41556-019-0425-z (2019). [CrossRef] [PubMed] [Google Scholar]
  9. Lander, E. S. The Heroes of CRISPR. Cell 164, 18-28, doi:10.1016/j.cell.2015.12.041 (2016). [CrossRef] [PubMed] [Google Scholar]
  10. Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S. & Gregory, P. D. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11, 636-646, doi:10.1038/nrg2842 (2010). [CrossRef] [PubMed] [Google Scholar]
  11. Buck-Koehntop, B. A. et al. Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Proc Natl Acad Sci U S A 109, 15229-15234, doi:10.1073/pnas.1213726109 (2012). [CrossRef] [PubMed] [Google Scholar]
  12. Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 188, 773-782, doi:10.1534/genetics.111.131433 (2011). [CrossRef] [PubMed] [Google Scholar]
  13. Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29, 143-148, doi:10.1038/nbt.1755 (2011). [CrossRef] [PubMed] [Google Scholar]
  14. Li, T. et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39, 359-372, doi:10.1093/nar/gkq704 (2011). [CrossRef] [PubMed] [Google Scholar]
  15. Juillerat, A. et al. Comprehensive analysis of the specificity of transcription activator-like effector nucleases. Nucleic Acids Res 42, 5390-5402, doi:10.1093/nar/gku155 (2014). [CrossRef] [PubMed] [Google Scholar]
  16. Sander, J. D. et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8, 67-69, doi:10.1038/nmeth.1542 (2011). [CrossRef] [PubMed] [Google Scholar]
  17. Maeder, M. L. et al. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31, 294-301, doi:10.1016/j.molcel.2008.06.016 (2008). [CrossRef] [PubMed] [Google Scholar]
  18. 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, 5429-5433, doi:10.1128/jb.169.12.5429-5433.1987 (1987). [CrossRef] [PubMed] [Google Scholar]
  19. Mojica, F. J., Diez-Villasenor, C., Soria, E. & Juez, G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 36, 244-246, doi:10.1046/j.1365-2958.2000.01838.x (2000). [CrossRef] [PubMed] [Google Scholar]
  20. Kunin, V., Sorek, R. & Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8, R61, doi:10.1186/gb-2007-8-4-r61 (2007). [Google Scholar]
  21. Jansen, R., Embden, J. D., Gaastra, W. & Schouls, L. M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43, 1565-1575, doi:10.1046/j.1365-2958.2002.02839.x (2002). [CrossRef] [PubMed] [Google Scholar]
  22. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821, doi:10.1126/science.1225829 (2012). [Google Scholar]
  23. Bolotin, A., Quinquis, B., Sorokin, A. & Ehrlich, S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561, doi:10.1099/mic.0.28048-0 (2005). [CrossRef] [PubMed] [Google Scholar]
  24. Barrangou, R. & Marraffini, L. A. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell 54, 234-244, doi:10.1016/j.molcel.2014.03.011 (2014). [CrossRef] [PubMed] [Google Scholar]
  25. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826, doi:10.1126/science.1232033 (2013). [Google Scholar]
  26. Gaj, T., Gersbach, C. A. & Barbas, C. F., 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31, 397-405, doi:10.1016/j.tibtech.2013.04.004 (2013). [CrossRef] [PubMed] [Google Scholar]
  27. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31, 233-239, doi:10.1038/nbt.2508 (2013). [CrossRef] [PubMed] [Google Scholar]
  28. Nunez, J. K. et al. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol 21, 528-534, doi:10.1038/nsmb.2820 (2014). [CrossRef] [PubMed] [Google Scholar]
  29. Chylinski, K., Le Rhun, A. & Charpentier, E. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol 10, 726-737, doi:10.4161/rna.24321 (2013). [Google Scholar]
  30. Karvelis, T. et al. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 10, 841-851, doi:10.4161/rna.24203 (2013). [Google Scholar]
  31. Wiedenheft, B. et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486-489, doi:10.1038/nature10402 (2011). [PubMed] [Google Scholar]
  32. Gleditzsch, D. et al. PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA Biol 16, 504-517, doi:10.1080/15476286.2018.1504546 (2019). [Google Scholar]
  33. 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, E2579-2586, doi:10.1073/pnas.1208507109 (2012). [CrossRef] [PubMed] [Google Scholar]
  34. Knott, G. J. & Doudna, J. A. CRISPR-Cas guides the future of genetic engineering. Science 361, 866-869, doi:10.1126/science.aat5011 (2018). [Google Scholar]
  35. Terns, M. P. & Terns, R. M. CRISPR-based adaptive immune systems. Curr Opin Microbiol 14, 321-327, doi:10.1016/j.mib.2011.03.005 (2011). [CrossRef] [PubMed] [Google Scholar]
  36. Song, M., Kim, Y. H., Kim, J. S. & Kim, H. Genome engineering in human cells. Methods Enzymol 546, 93-118, doi:10.1016/B978-0-12-801185-0.00005-2 (2014). [Google Scholar]
  37. Jasin, M. & Rothstein, R. Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol 5, a012740, doi:10.1101/cshperspect.a012740 (2013). [Google Scholar]
  38. Kim, Y. G., Cha, J. & Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93, 1156-1160, doi:10.1073/pnas.93.3.1156 (1996). [CrossRef] [PubMed] [Google Scholar]
  39. Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol 25, 786-793, doi:10.1038/nbt1317 (2007). [CrossRef] [PubMed] [Google Scholar]
  40. Jiang, F. & Doudna, J. A. CRISPR-Cas9 Structures and Mechanisms. Annu Rev Biophys 46, 505-529, doi:10.1146/annurev-biophys-062215-010822 (2017). [CrossRef] [PubMed] [Google Scholar]
  41. Wiedenheft, B. et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A 108, 10092-10097, doi:10.1073/pnas.1102716108 (2011). [CrossRef] [PubMed] [Google Scholar]
  42. Mojica, F. J. M., Diez-Villasenor, C., Garcia-Martinez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740, doi:10.1099/mic.0.023960-0 (2009). [CrossRef] [PubMed] [Google Scholar]
  43. Marraffini, L. A. & Sontheimer, E. J. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568-571, doi:10.1038/nature08703 (2010). [PubMed] [Google Scholar]
  44. Esvelt, K. M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10, 1116-1121, doi:10.1038/nmeth.2681 (2013). [CrossRef] [PubMed] [Google Scholar]
  45. Fonfara, I. et al. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 42, 2577-2590, doi:10.1093/nar/gkt1074 (2014). [CrossRef] [PubMed] [Google Scholar]
  46. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997, doi:10.1126/science.1247997 (2014). [Google Scholar]
  47. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949, doi:10.1016/j.cell.2014.02.001 (2014). [CrossRef] [PubMed] [Google Scholar]
  48. Palella, F. J., Jr. et al. Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. N Engl J Med 338, 853-860, doi:10.1056/NEJM199803263381301 (1998). [Google Scholar]
  49. Gandhi, R. T. et al. The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLoS Med 7, doi:10.1371/journal.pmed.1000321 (2010). [Google Scholar]
  50. Finzi, D. et al. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278, 1295-1300, doi:10.1126/science.278.5341.1295 (1997). [Google Scholar]
  51. Chun, T. W. et al. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387, 183-188, doi:10.1038/387183a0 (1997). [PubMed] [Google Scholar]
  52. Mougel, M., Houzet, L. & Darlix, J. L. When is it time for reverse transcription to start and go? Retrovirology 6, 24, doi:10.1186/1742-4690-6-24 (2009). [CrossRef] [PubMed] [Google Scholar]
  53. Wong, J. K. et al. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278, 1291-1295, doi:10.1126/science.278.5341.1291 (1997). [Google Scholar]
  54. Siliciano, J. D. et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med 9, 727-728, doi:10.1038/nm880 (2003). [CrossRef] [PubMed] [Google Scholar]
  55. Hermankova, M. et al. Analysis of human immunodeficiency virus type 1 gene expression in latently infected resting CD4+ T lymphocytes in vivo. J Virol 77, 7383-7392, doi:10.1128/jvi.77.13.7383-7392.2003 (2003). [CrossRef] [PubMed] [Google Scholar]
  56. Kaminski, R. et al. Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing. Sci Rep 6, 22555, doi:10.1038/srep22555 (2016). [CrossRef] [PubMed] [Google Scholar]
  57. Ebina, H., Misawa, N., Kanemura, Y. & Koyanagi, Y. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep 3, 2510, doi:10.1038/srep02510 (2013). [CrossRef] [PubMed] [Google Scholar]
  58. Craigie, R. & Bushman, F. D. HIV DNA integration. Cold Spring Harb Perspect Med 2, a006890, doi:10.1101/cshperspect.a006890 (2012). [Google Scholar]
  59. Liao, H. K. et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun 6, 6413, doi:10.1038/ncomms7413 (2015). [Google Scholar]
  60. O’Neil, P. K. et al. Mutational analysis of HIV-1 long terminal repeats to explore the relative contribution of reverse transcriptase and RNA polymerase II to viral mutagenesis. J Biol Chem 277, 38053-38061, doi:10.1074/jbc.M204774200 (2002). [CrossRef] [PubMed] [Google Scholar]
  61. Rodriguez, M. A. et al. Genetic and functional characterization of the LTR of HIV-1 subtypes A and C circulating in India. AIDS Res Hum Retroviruses 23, 1428-1433, doi:10.1089/aid.2007.0152 (2007). [CrossRef] [PubMed] [Google Scholar]
  62. Hu, W. et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci U S A 111, 11461-11466, doi:10.1073/pnas.1405186111 (2014). [CrossRef] [PubMed] [Google Scholar]
  63. Kaminski, R. et al. Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther 23, 690-695, doi:10.1038/gt.2016.41 (2016). [CrossRef] [PubMed] [Google Scholar]
  64. Soriano, V. Hot News: Gene Therapy with CRISPR/Cas9 Coming to Age for HIV Cure. AIDS Rev 19, 167-172 (2017). [Google Scholar]
  65. 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, 819-830, doi:10.1517/14712598.2015.1036736 (2015). [PubMed] [Google Scholar]
  66. Bleul, C. C., Wu, L., Hoxie, J. A., Springer, T. A. & Mackay, C. R. The HIV coreceptors CXCR4 and CCR5 are differentially expressed and regulated on human T lymphocytes. Proc Natl Acad Sci U S A 94, 1925-1930, doi:10.1073/pnas.94.5.1925 (1997). [CrossRef] [PubMed] [Google Scholar]
  67. Nagasawa, T. et al. Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1. Nature 382, 635-638, doi:10.1038/382635a0 (1996). [PubMed] [Google Scholar]
  68. Samson, M. et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722-725, doi:10.1038/382722a0 (1996). [PubMed] [Google Scholar]
  69. Allers, K. et al. Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation. Blood 117, 2791-2799, doi:10.1182/blood-2010-09-309591 (2011). [Google Scholar]
  70. Hutter, G. et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med 360, 692-698, doi:10.1056/NEJMoa0802905 (2009). [Google Scholar]
  71. Biti, R. et al. HIV-1 infection in an individual homozygous for the CCR5 deletion allele. Nat Med 3, 252-253, doi:10.1038/nm0397-252 (1997). [CrossRef] [PubMed] [Google Scholar]
  72. Cho, S. W., Kim, S., Kim, J. M. & Kim, J. S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31, 230-232, doi:10.1038/nbt.2507 (2013). [CrossRef] [PubMed] [Google Scholar]
  73. Zimmerman, P. A. et al. Inherited resistance to HIV-1 conferred by an inactivating mutation in CC chemokine receptor 5: studies in populations with contrasting clinical phenotypes, defined racial background, and quantified risk. Mol Med 3, 23-36 (1997). [CrossRef] [PubMed] [Google Scholar]
  74. Holt, N. et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nat Biotechnol 28, 839-847, doi:10.1038/nbt.1663 (2010). [CrossRef] [PubMed] [Google Scholar]
  75. Perez, E. E. et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26, 808-816, doi:10.1038/nbt1410 (2008). [CrossRef] [PubMed] [Google Scholar]
  76. Xu, L. et al. CRISPR/Cas9-Mediated CCR5 Ablation in Human Hematopoietic Stem/Progenitor Cells Confers HIV-1 Resistance In Vivo. Mol Ther 25, 1782-1789, doi:10.1016/j.ymthe.2017.04.027 (2017). [CrossRef] [PubMed] [Google Scholar]
  77. Xiao, Q., Guo, D. & Chen, S. Application of CRISPR/Cas9-Based Gene Editing in HIV-1/AIDS Therapy. Front Cell Infect Microbiol 9, 69, doi:10.3389/fcimb.2019.00069 (2019). [CrossRef] [PubMed] [Google Scholar]
  78. Lino, C. A., Harper, J. C., Carney, J. P. & Timlin, J. A. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv 25, 1234-1257, doi:10.1080/10717544.2018.1474964 (2018). [CrossRef] [PubMed] [Google Scholar]
  79. Xu, C. L., Ruan, M. Z. C., Mahajan, V. B. & Tsang, S. H. Viral Delivery Systems for CRISPR. Viruses 11, doi:10.3390/v11010028 (2019). [Google Scholar]
  80. Wang, W. et al. CCR5 gene disruption via lentiviral vectors expressing Cas9 and single guided RNA renders cells resistant to HIV-1 infection. PLoS One 9, e115987, doi:10.1371/journal.pone.0115987 (2014). [Google Scholar]
  81. Cradick, T. J., Fine, E. J., Antico, C. J. & Bao, G. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41, 9584-9592, doi:10.1093/nar/gkt714 (2013). [CrossRef] [PubMed] [Google Scholar]

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