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18 - Genome Editing of Pluripotent Stem Cells

from Part IV - Genome Editing in Stem Cells and Regenerative Biology

Published online by Cambridge University Press:  30 July 2018

By
Zhili Rong  and
Yang Xu
Edited by
Krishnarao Appasani
Foreword by
George M. Church
Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
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Type
Chapter
Information
Genome Editing and Engineering
From TALENs, ZFNs and CRISPRs to Molecular Surgery
 , pp. 270 - 284
Publisher: Cambridge University Press
Print publication year: 2018

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References

Abudayyeh, OO, Gootenberg, JS, Konermann, S, et al. 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353: aaf5573.CrossRefGoogle ScholarPubMed
Avior, Y, Sagi, I, Benvenisty, N. 2016. Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol 17: 170–182.CrossRefGoogle ScholarPubMed
Barrangou, R, Doudna, JA. 2016. Applications of CRISPR technologies in research and beyond. Nat Biotech 34: 933–941.CrossRefGoogle ScholarPubMed
Beerli, RR, Segal, DJ, Dreier, B, Barbas, CF III. 1998. 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 95: 14628–14633.CrossRefGoogle ScholarPubMed
Bhakta, MS, Henry, IM, Ousterout, DG, et al. 2013. Highly active zinc-finger nucleases by extended modular assembly. Genome Res 23: 530–538.CrossRefGoogle ScholarPubMed
Bibikova, M, Beumer, K, Trautman, JK, Carroll, D. 2003. Enhancing gene targeting with designed zinc finger nucleases. Science 300: 764.CrossRefGoogle ScholarPubMed
Boch, J, Scholze, H, Schornack, S, et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 1509–1512.CrossRefGoogle ScholarPubMed
Bolukbasi, MF, Gupta, A, Oikemus, S, et al. 2015. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods 12: 1150–1156.CrossRefGoogle ScholarPubMed
Braam, SR, Tertoolen, L, Van De Stolpe, A, et al. 2010. Prediction of drug-induced cardiotoxicity using human embryonic stem cell-derived cardiomyocytes. Stem Cell Res 4: 107–116.CrossRefGoogle ScholarPubMed
Capecchi, MR. 1989. Altering the genome by homologous recombination. Science 244: 1288–1292.CrossRefGoogle ScholarPubMed
Carroll, D. 2014. Genome engineering with targetable nucleases. Annu Rev Biochem 83: 409–439.CrossRefGoogle ScholarPubMed
Chung, SK, Zhu, S, Xu, Y, Fu, X. 2014. Functional analysis of the acetylation of human p53 in DNA damage responses. Protein Cell 5: 544–551.CrossRefGoogle ScholarPubMed
Davis, RP, Ng, ES, Costa, M, et al. 2008. Targeting a GFP reporter gene to the MIXL1 locus of human embryonic stem cells identifies human primitive streak-like cells and enables isolation of primitive hematopoietic precursors. Blood 111: 1876–1884.CrossRefGoogle Scholar
De Los Angeles, A, Ferrari, F, Xi, R, et al. 2015. Hallmarks of pluripotency. Nature 525: 469–478.CrossRefGoogle ScholarPubMed
Dominguez, AA, Lim, WA, Qi, LS. 2016. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 17: 5–15.CrossRefGoogle ScholarPubMed
Doudna, JA, Charpentier, E. 2014. Genome editing: the new frontier of genome engineering with CRISPR-Cas9. Science 346: 1258096.CrossRefGoogle ScholarPubMed
East-Seletsky, A, O’Connell, MR, Knight, SC, et al. 2016. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538(7624): 270–273.CrossRefGoogle ScholarPubMed
Fu, X, Rong, Z, Zhu, S, et al. 2014a. Genetic approach to track neural cell fate decisions using human embryonic stem cells. Protein Cell 5: 69–79.CrossRefGoogle ScholarPubMed
Fu, Y, Sander, JD, Reyon, D, Cascio, VM, Joung, JK. 2014b. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32: 279–284.CrossRefGoogle ScholarPubMed
Gersbach, CA, Gaj, T, Gordley, RM, Mercer, AC, Barbas, CF III. 2011. Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase. Nucleic Acids Res 39: 7868–7878.CrossRefGoogle ScholarPubMed
Guilinger, JP, Thompson, DB, Liu, DR 2014. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32: 577–582.CrossRefGoogle ScholarPubMed
Gupta, A, Christensen, RG, Rayla, AL, et al. 2012. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 9: 588–590.CrossRefGoogle ScholarPubMed
Hsu, PD, Lander, ES, Zhang, F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157: 1262–1278.CrossRefGoogle Scholar
Khan, IF, Hirata, RK, Russell, DW. 2011. AAV-mediated gene targeting methods for human cells. Nat Protoc 6: 482–501.CrossRefGoogle ScholarPubMed
Khan, IF, Hirata, RK, Wang, PR, et al. 2010. Engineering of human pluripotent stem cells by AAV-mediated gene targeting. Mol Ther 18: 1192–1199.CrossRefGoogle ScholarPubMed
Kleinstiver, BP, Pattanayak, V, Prew, MS, et al. 2016. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529: 490–495.CrossRefGoogle ScholarPubMed
Koller, BH, Smithies, O. 1992. Altering genes in animals by gene targeting. Annu Rev Immunol 10: 705–730.CrossRefGoogle ScholarPubMed
Konermann, S, Brigham, MD, Trevino, AE, et al. 2015. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517: 583–588.CrossRefGoogle ScholarPubMed
Lancaster, MA, Knoblich, JA. 2014. Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345: 1247125.CrossRefGoogle Scholar
Liu, GH, Qu, J, Suzuki, K, et al. 2012. Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature 491: 603–607.CrossRefGoogle ScholarPubMed
Liu, GH, Suzuki, K, Qu, J, et al. 2011. Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. Cell Stem Cell 8: 688–694.CrossRefGoogle ScholarPubMed
Maeder, ML, Thibodeau-Beganny, S, Osiak, A, et al. 2008. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31: 294–301.CrossRefGoogle ScholarPubMed
Moscou, MJ, Bogdanove, AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501.CrossRefGoogle ScholarPubMed
Porteus, MH, Baltimore, D. 2003. Chimeric nucleases stimulate gene targeting in human cells. Science 300: 763.CrossRefGoogle ScholarPubMed
Ramirez, CL, Foley, JE, Wright, DA, et al. 2008. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods 5: 374–375.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Lin, CY, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380–1389.CrossRefGoogle ScholarPubMed
Rong, Z, Fu, X, Wang, M, Xu, Y. 2012. A scalable approach to prevent teratoma formation of human embryonic stem cells. J Biol Chem 287: 32338–32345.CrossRefGoogle ScholarPubMed
Rong, Z, Wang, M, Hu, Z, et al. 2014. An effective approach to prevent immune rejection of human ESC-derived allografts. Cell Stem Cell 14: 121–130.CrossRefGoogle ScholarPubMed
Sander, JD, Dahlborg, EJ, Goodwin, MJ, et al. 2011. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8: 67–69.CrossRefGoogle ScholarPubMed
Schwartz, SD, Regillo, CD, Lam, BL, et al. 2015. Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet 385: 509–516.CrossRefGoogle ScholarPubMed
Shalem, O, Sanjana, NE, Zhang, F. 2015. High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet 16: 299–311.CrossRefGoogle ScholarPubMed
Shechner, DM, Hacisuleyman, E, Younger, ST, Rinn, JL. 2015. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods 12: 664–670.CrossRefGoogle ScholarPubMed
Shmakov, S, Abudayyeh, OO, Makarova, KS, et al. 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60: 385–397.CrossRefGoogle ScholarPubMed
Slaymaker, IM, Gao, L, Zetsche, B, et al. 2016. Rationally engineered Cas9 nucleases with improved specificity. Science 351: 84–88.CrossRefGoogle ScholarPubMed
Soldner, F, Laganiere, J, Cheng, AW, et al. 2011. Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell 146: 318–331.CrossRefGoogle ScholarPubMed
Song, H, Chung, SK, Xu, Y. 2010. Modeling disease in human ESCs using an efficient BAC-based homologous recombination system. Cell Stem Cell 6: 80–89.CrossRefGoogle ScholarPubMed
Symington, LS, Gautier, J. 2011. Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247–271.CrossRefGoogle ScholarPubMed
Tebas, P, Stein, D, Tang, WW, et al. 2014. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med 370: 901–910.CrossRefGoogle ScholarPubMed
Thakore, PI, Black, JB, Hilton, IB, Gersbach, CA. 2016. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods 13: 127–137.CrossRefGoogle ScholarPubMed
Trounson, A, Dewitt, ND. 2016. Pluripotent stem cells progressing to the clinic. Nat Rev Mol Cell Biol 17: 194–200.CrossRefGoogle ScholarPubMed
Tsai, SQ, Wyvekens, N, Khayter, C, et al. 2014. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32: 569–576.CrossRefGoogle ScholarPubMed
Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS, Gregory, PD. 2010. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11: 636–646.CrossRefGoogle ScholarPubMed
Xue, H, Wu, S, Papadeas, ST, et al. 2009. A targeted neuroglial reporter line generated by homologous recombination in human embryonic stem cells. Stem Cells 27: 1836–1846.CrossRefGoogle ScholarPubMed
Yang, Y, Wang, L, Bell, P, et al. 2016. A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice. Nat Biotechnol 34: 334–338.CrossRefGoogle ScholarPubMed
Yant, SR, Huang, Y, Akache, B, Kay, MA. 2007. Site-directed transposon integration in human cells. Nucleic Acids Res 35: e50.CrossRefGoogle ScholarPubMed
Yusa, K, Rashid, ST, Strick-Marchand, H, et al. 2011. Targeted gene correction of alpha1-antitrypsin deficiency in induced pluripotent stem cells. Nature 478: 391–394.CrossRefGoogle ScholarPubMed
Zalatan, JG, Lee, ME, Almeida, R, et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160: 339–350.CrossRefGoogle ScholarPubMed
Zetsche, B, Gootenberg, JS, Abudayyeh, OO, et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163: 759–771.CrossRefGoogle ScholarPubMed
Zhu, Z, Li, QV, Lee, K, et al. 2016. Genome editing of lineage determinants in human pluripotent stem cells reveals mechanisms of pancreatic development and diabetes. Cell Stem Cell 18: 755–768.CrossRefGoogle ScholarPubMed
Zwaka, TP, Thomson, JA. 2003. Homologous recombination in human embryonic stem cells. Nat Biotechnol 21: 319–321.CrossRefGoogle ScholarPubMed

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