Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System (original) (raw)

References

  1. Sebat, J., Levy, D. L., & McCarthy, S. E. (2009). Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. Trends in Genetics, 25, 528–535.
    Article PubMed Central CAS PubMed Google Scholar
  2. Dipple, K. M., & McCabe, E. R. (2000). Phenotypes of patients with “simple” Mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics. American Journal of Human Genetics, 66, 1729–1735.
    Article PubMed Central CAS PubMed Google Scholar
  3. Musunuru, K. (2013). Genome editing of human pluripotent stem cells to generate human cellular disease models. Disease Models & Mechanisms, 6, 896–904.
    Article CAS Google Scholar
  4. Kim, H., Jang, M. J., Kang, M. J., & Han, Y. M. (2011). Epigenetic signatures and temporal expression of lineage-specific genes in hESCs during differentiation to hepatocytes in vitro. Human Molecular Genetics, 20, 401–412.
    Article CAS PubMed Google Scholar
  5. Lister, R., Pelizzola, M., Kida, Y. S., et al. (2011). Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 471, 68–73.
    Article PubMed Central CAS PubMed Google Scholar
  6. Ruiz, S., Diep, D., Gore, A., et al. (2012). Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America, 109, 16196–16201.
    Article PubMed Central CAS PubMed Google Scholar
  7. Zwaka, T. P., & Thomson, J. A. (2003). Homologous recombination in human embryonic stem cells. Nature Biotechnology, 21, 319–321.
    Article CAS PubMed Google Scholar
  8. Placantonakis, D. G., Tomishima, M. J., Lafaille, F., et al. (2009). BAC transgenesis in human embryonic stem cells as a novel tool to define the human neural lineage. Stem Cells, 27, 521–532.
    Article CAS PubMed Google Scholar
  9. Song, H., Chung, S. K., & Xu, Y. (2010). Modeling disease in human ESCs using an efficient BAC-based homologous recombination system. Cell Stem Cell, 6, 80–89.
    Article CAS PubMed Google Scholar
  10. Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013). RNA-programmed genome editing in human cells. eLife, 2, e00471.
    Article PubMed Central PubMed Google Scholar
  11. Cong, L., Ran, F. A., Cox, D., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science (New York, NY), 339, 819–823.
    Article CAS Google Scholar
  12. Mali, P., Yang, L., Esvelt, K. M., et al. (2013). RNA-guided human genome engineering via Cas9. Science (New York, NY), 339, 823–826.
    Article CAS Google Scholar
  13. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (New York, NY), 337, 816–821.
    Article CAS Google Scholar
  14. Lin, S., Staahl, B. T., Alla, R. K., & Doudna, J. A. (2014). Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife, 3, e04766.
    PubMed Google Scholar
  15. Chen, F., Pruett-Miller, S. M., Huang, Y., et al. (2011). High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nature Methods, 8, 753–755.
    Article PubMed Central CAS PubMed Google Scholar
  16. Doench, J. G., Hartenian, E., Graham, D. B., et al. (2014). Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology, 32, 1262–1267.
    Article PubMed Central CAS PubMed Google Scholar
  17. Huang, X., Wang, Y., Yan, W., et al. (2015). Production of gene-corrected adult beta globin protein in human erythrocytes differentiated from patient iPSCs after genome editing of the sickle point mutation. Stem Cells, 33, 1470–1479.
    Article CAS PubMed Google Scholar
  18. Li, H. L., Fujimoto, N., Sasakawa, N., et al. (2015). Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Reports, 4, 143–154.
    Article PubMed Central CAS PubMed Google Scholar
  19. Miyaoka, Y., Chan, A. H., Judge, L. M., et al. (2014). Isolation of single-base genome-edited human iPS cells without antibiotic selection. Nature Methods, 11, 291–293.
    Article PubMed Central CAS PubMed Google Scholar
  20. Reinhardt, P., Schmid, B., Burbulla, L. F., et al. (2013). Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneration to ERK-dependent changes in gene expression. Cell Stem Cell, 12, 354–367.
    Article CAS PubMed Google Scholar
  21. Soldner, F., Laganiere, J., Cheng, A. W., et al. (2011). Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell, 146, 318–331.
    Article PubMed Central CAS PubMed Google Scholar
  22. Ye, L., Wang, J., Beyer, A. I., et al. (2014). Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Delta32 mutation confers resistance to HIV infection. Proceedings of the National Academy of Sciences of the United States of America, 111, 9591–9596.
    Article PubMed Central CAS PubMed Google Scholar
  23. Yusa, K. (2013). Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon. Nature Protocols, 8, 2061–2078.
    Article CAS PubMed Google Scholar
  24. Wen, Z., Nguyen, H. N., Guo, Z., et al. (2014). Synaptic dysregulation in a human iPS cell model of mental disorders. Nature, 515, 414–418.
    Article PubMed Central CAS PubMed Google Scholar
  25. Guschin, D. Y., Waite, A. J., Katibah, G. E., Miller, J. C., Holmes, M. C., & Rebar, E. J. (2010). A rapid and general assay for monitoring endogenous gene modification. Methods in Molecular Biology, 649, 247–256.
    Article CAS PubMed Google Scholar
  26. Froger, A., Hall, J. E. (2007). Transformation of plasmid DNA into E. coli using the heat shock method. Journal of Visualized Experiments: JoVE, 253.
  27. Vouillot, L., Thelie, A., & Pollet, N. (2015). Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3, 5, 407–415.
    Article PubMed Central PubMed Google Scholar
  28. Smithies, O., Gregg, R. G., Boggs, S. S., Koralewski, M. A., & Kucherlapati, R. S. (1985). Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination. Nature, 317, 230–234.
    Article CAS PubMed Google Scholar
  29. Hasty, P., Rivera-Perez, J., & Bradley, A. (1991). The length of homology required for gene targeting in embryonic stem cells. Molecular and Cellular Biology, 11, 5586–5591.
    PubMed Central CAS PubMed Google Scholar
  30. Lin, Y., Cradick, T. J., Brown, M. T., et al. (2014). CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Research, 42, 7473–7485.
    Article PubMed Central CAS PubMed Google Scholar
  31. Takahashi, K., Tanabe, K., Ohnuki, M., et al. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131, 861–872.
    Article CAS PubMed Google Scholar
  32. Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012). Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 109, E2579–E2586.
    Article PubMed Central CAS PubMed Google Scholar
  33. Ran, F. A., Hsu, P. D., Lin, C. Y., et al. (2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154, 1380–1389.
    Article PubMed Central CAS PubMed Google Scholar

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