Combinatorial gene editing in mammalian cells using ssODNs and TALENs

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Strouse, Bryan ^a   Bialk, Pawel ^a   Niamat, Rohina A ^a   Rivera Torres, Natalia ^a   Kmiec, Eric B ^a  

^a DELAWARE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; OLIGONUCLEOTIDE;

ANIMAL; ARTICLE; CHEMISTRY; DNA REPLICATION; GENE TARGETING; GENETICS; HCT116 CELL LINE; HUMAN; TRANSCRIPTION INITIATION;

ANIMALS; DEOXYRIBONUCLEASES; DNA REPLICATION; GENE TARGETING; HCT116 CELLS; HUMANS; OLIGONUCLEOTIDES; TRANSCRIPTIONAL ACTIVATION;

EID: 84900311030     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03791     Document Type: Article

References (40)

1. Parekh-Olmedo, H. & Kmiec, E. B. Progress and prospects: targeted gene alteration (TGA). Gene Ther. 14, 1675-1680 (2007).
2. Engstrom, J. U., Suzuki, T. & Kmiec, E. B. Regulation of targeted gene repair by intrinsic cellular processes. BioEssays. 31, 159-168 (2009).
3. Aarts, M. & te Riele, H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther. 18, 213-219 (2011).
4. Ferrara, L. & Kmiec, E. B. Targeted gene repair activates chk1 and chk2 and stalls replication in corrected cells. DNA repair (Amst). 5, 422-431 (2006).
5. Ferrara, L., Engstrom, J. U., Schwartz, T., Parekh-Olmedo, H. & Kmiec, E. B. Recovery of cell cycle delay following targeted gene repair by oligonucleotides. DNA Repair (Amst). 6, 1529-1535 (2007).
6. Ferrara, L., Parekh-Olmedo, H. & Kmiec, E. B. DNA damage increases the frequency of gene repair in mammalian cells. Experimental Cell Res. 300, 170-179 (2004).
7. Ferrara, L. & Kmiec, E. B. Camptothecin enhances the frequency of oligonucleotide-directed gene repair in mammalian cells by inducing DNA damage and activating homologous recombination. Nucleic Acids Res. 32, 5239-5248 (2004).
8. Radecke, F. et al. Targeted chromosomal gene modification in human cells by single-stranded oligodeoxynucleotides in the presence of a DNA double-strand break. Mol Ther. 14, 298-808 (2006).
9. Olsen, P. A., Randol, M. & Krauss, S. Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides. Gene Ther. 12, 546-551 (2005).
10. Engstrom, J. & Kmiec, E. B. DNA Replication, Cell Cycle Progression and the Targeted Gene Repair Reaction. Cell Cycle. 28, 1402-1414 (2008).
11. Brachman, E. & Kmiec, E. B. Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks. DNA Repair (Amst). 4, 445-457 (2005).
12. Huen, M. S. et al. The involvement of replication in single-stranded oligonucleotide-mediated gene repair. Nucleic Acids Res. 34, 6183-6194 (2006).
13. Olsen, P. A., Randol, M., Luna, L., Brown, T. & Kraus, S. Genomic sequence correction by single-stranded DNA oligonucleotides: role of DNA synthesis and chemical modifications of the oligonucleotide ends. J Gene Med. 7, 1534-1544 (2005).
14. Radecke, S., Radecke, F., Peter, I. & Schwarz, K. Physical incorporation of a singlestranded oligodeoxynucleotides during targeted repair of a human chromosomal locus. J Gene Med. 8, 217-228 (2006).
15. Radecke, F., Radecke, S.& Schwarz, K. Unmodified oligodeoxynucleotides require single-strandedness to induce targeted repair of a chromosomal EGFP gene. J Gene Med. 6, 1257-1271 (2004).
16. Papaioannou, I., Disterer, P. & Owens, J. S. Use of internally nuclease protected single-strand DNA oligonucleotides and silencing of the mismatch repair protein, MSH2, enhances the replication of corrected cells following gene editing. J Gene Med. 11, 267-274 (2009).
17. Bonner, M., Strouse, B., Applegate, M., Livingston, P.&Kmiec, E. B.DNAdamage response pathway and replication fork stress during oligonucleotide directed gene editing. Mol Ther. 1, e18 (2012).
18. Borjigin,M. et al. Proliferation of genetically modified human cells on electrospun nanofiber scaffolds. Mol Ther. 1, 10.1038 (2012).
19. Livingston, P. et al. Oligonucleotide delivery by Nucleofection does not rescue the Reduced Proliferation Phenotype in gene-edited cells. Nucl Acids Ther. 22, 405-413 (2012).
20. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39(12), e82 (2011).
21. Doyle, E. L. et al. TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40, 117-122 (2012).
22. Bedell, V. M. et al. In vivo genome editing using a high-efficiency TALEN system. Nature. 491(7422), 114-8 (2012).
23. Bonner, M. & Kmiec, E. B. DNA breakage associated with targeted gene alteration directed by DNA oligonucleotides. Mutat Res. 669(1-2), 85-94 (2009).
24. Mak, A. N.-S., Bradley, P., Cernadas, R. A., Bogdanove, A. J. & Stoddard, B. L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science. 335, 716-719 (2012).
25. Deng, D. et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 335, 720-723 (2012).
26. Andersen, M. S., Sorensen, C. B., Bolund, L. & Jensen, T. G. Mechanisms underlying targeted gene correction using chimeric RNA/DNA and singlestranded DNA oligonucleotides. J Mol Med. 80, 770-781 (2002).
27. Brachman, E. E. & Kmiec, E. B. The biased evolution of targeted gene repair. Curr Opin Mol Ther. 3, 171-176 (2002).
28. Liu, L. et al. Strand bias in targeted gene repair is influenced by transcriptional activity. Mol Cell Biol. 22, 3852-3863 (2002).
29. Igoucheva, O., Alexeev, V. & Yoon, K. Targeted gene correction by small singlestranded oligonucleotides in mammalian cells. Gene Ther. 5, 391-399 (2001).
30. Liu, L., Parekh-Olmedo, H. & Kmiec, E. B. Development and regulation of gene repair. Nat Rev Genet. 4, 679-689 (2003).
31. Wu, X. S. et al. Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression. Proc Natl Acad Sci USA. 102, 2508-2513 (2005).
32. Engstrom, J. U. & Kmiec, E. B. Manipulation of cell cycle progression can counteract the apparent loss of correction frequency following oligonucleotidedirected gene repair. BMC Mol Biol. 8, 9 (2007).
33. Parekh-Olmedo, H., Engstrom, J. & Kmiec, E. B. The effect of hydroxyurea and trichostatin A on targeted nucleotide exchange in yeast and mammalian cells. New York Academy of Science. 1002, 43-56 (2003).
34. Wefers, B. et al. Direct microinjection of mouse disease models by embryo microinjection of TALENs and ODNs. Pro Natl Acad Sci. 10, 1073 (2013).
35. Ding, Q. et al. A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models. Cell Stem Cell. 12, 1-14 (2013).
36. Briggs, A. W. et al. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucl. Acids Res. 40, 5 e117 (2012).
37. Liu, J., Majumdar, A., Liu, J., Thompson, L. H. & Seidman, M. M. Sequence conversion of single stranded oligonucleotide donors via non-homologous end joining in mammalian cells. J. Biol. Chem. 285(30), 23198-23207 (2010).
38. Majumdar, A. et al. Cell cycle modulation of gene targeting by a triple helixforming oligonucleotide. J. Biol. Chem. 278, 11072-11077 (2003).
39. Morozov, V. & Wawrousek, E. F. Single-strand DNA-mediated targeted mutagenesis of genomic DNA in early mouse embryos is stimulated by Rad51/54 and by Ku70/86 inhibition. Gene Ther. 15, 468-472 (2003).
40. Yang, L. et al. Optimization of scarless human stem cell genome editing. Nucleic Acids Res, 10, 1-13 (2013).