Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome

Genome Research

Volumn 20, Issue 8, 2010, Pages 1133-1142

  DeKelver, Russell C ^a   Choi, Vivian M ^a   Moehle, Erica A ^a   Paschon, David E ^a   Hockemeyer, Dirk ^b   Meijsing, Sebastiaan H ^c,f   Sancak, Yasemin ^b   Cui, Xiaoxia ^d   Steine, Eveline J ^b   Miller, Jeffrey C ^a   Tam, Phillip ^a   Bartsevich, Victor V ^a   Meng, Xiangdong ^a   Rupniewski, Igor ^a   Gopalan, Sunita M ^a   Sun, Helena C ^a   Pitz, Kathleen J ^a   Rock, Jeremy M ^a   Zhang, Lei ^a   Davis, Gregory D ^d   Rebar, Edward J ^a   Cheeseman, Iain M ^e   Yamamoto, Keith R ^c   Sabatini, David M ^b   Jaenisch, Rudolf ^b,e   Gregory, Philip D ^a   Urnov, Fyodor D ^a   more..

^a SANGAMO BIOSCIENCES INC   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Sigma Aldrich Co   (United States)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; NUCLEASE; SHORT HAIRPIN RNA; UNCLASSIFIED DRUG; ZINC FINGER NUCLEASE;

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; FUNCTIONAL GENOMICS; GENE; GENE LOCUS; HUMAN; HUMAN CELL; HUMAN GENOME; PPP1R12C GENE; PRIORITY JOURNAL; PROTEOMICS; REGULATORY DNA SEQUENCE; TRANSGENICS;

BASE SEQUENCE; CELL LINE; ENDONUCLEASES; GENE TRANSFER TECHNIQUES; GENETIC LOCI; GENOME, HUMAN; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PROTEOMICS; REGULATORY SEQUENCES, NUCLEIC ACID; ZINC FINGERS;

EID: 77955157281     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.106773.110     Document Type: Article

References (44)

1. Berns K, Horlings HM, Hennessy BT, Madiredjo M, Hijmans EM, Beelen K, Linn SC, Gonzalez-Angulo AM, Stemke-Hale K, Hauptmann M, et al. 2007. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell 12: 395-402. (Pubitemid 47539306)
2. Bibikova M, Carroll D, Segal DJ, Trautman JK, Smith J, Kim YG, Chandrasegaran S. 2001. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21: 289-297.
3. Boley SE, McManus TP, Maher VM, McCormick JJ. 2000. Malignant transformation of human fibroblast cell strain MSU-1.1 by N-methyl-N- nitrosourea: Evidence of elimination of p53 by homologous recombination. Cancer Res 60: 4105-4111.
4. Carroll D. 2008. Progress and prospects: Zinc-finger nucleases as gene therapy agents. Gene Ther 15: 1463-1468.
5. Choo Y, Klug A. 1994. Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage. Proc Natl Acad Sci 91: 11163-11167. (Pubitemid 24349646)
6. Costa M, Dottori M, Sourris K, Jamshidi P, Hatzistavrou T, Davis R, Azzola L, Jackson S, Lim SM, Pera M, et al. 2007. A method for genetic modification of human embryonic stem cells using electroporation. Nat Protoc 2: 792-796. (Pubitemid 46745575)
7. Fang J, Qian JJ, Yi S, Harding TC, Tu GH, VanRoey M, Jooss K. 2005. Stable antibody expression at therapeutic levels using the 2A peptide. Nat Biotechnol 23: 584-590. (Pubitemid 41724897)
8. Gerber AN, Masuno K, Diamond MI. 2009. Discovery of selective glucocorticoid receptor modulators by multiplexed reporter screening. Proc Natl Acad Sci 106: 4929-4934.
9. Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, Jenkins SS, Wood A, Cui X, Meng X, et al. 2009. Knockout rats via embryo microinjection of zinc-finger nucleases. Science 325: 433. doi: 10.1126/science.1172447.
10. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
11. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, et al. 2010. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140: 678-691.
12. Hager GL, McNally JG, Misteli T. 2009. Transcription dynamics. Mol Cell 35: 741-753.
13. Hockemeyer D, Soldner F, Cook EG, Gao Q, Mitalipova M, Jaenisch R. 2008. A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Cell Stem Cell 3: 346-353.
14. Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, DeKelver RC, Katibah GE, Amora R, Boydston EA, Zeitler B, et al. 2009. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 27: 851-857.
15. Kayne PS, Kim UJ, Han M, Mullen JR, Yoshizaki F, Grunstein M. 1988. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell 55: 27-39.
16. Kohli M, Rago C, Lengauer C, Kinzler KW, Vogelstein B. 2004. Facile methods for generating human somatic cell gene knockouts using recombinant adeno-associated viruses. Nucleic Acids Res 32: e3. doi: 10.1093/nar/gnh009.
17. Kotin RM, Linden RM, Berns KI. 1992. Characterization of a preferred site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO J 11: 5071-5078.
18. Liu PQ, Chan EM, Cost GJ, Zhang L, Wang J, Miller JC, Guschin DY, Reik A, Holmes MC, Mott JE, et al. 2010. Generation of a triple-gene knockout mammalian cell line using engineered zinc-finger nucleases. Biotechnol Bioeng 106: 97-105.
19. Lombardo A, Genovese P, Beausejour CM, Colleoni S, Lee YL, Kim KA, Ando D, Urnov FD, Galli C, Gregory PD, et al. 2007. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25: 1298-1306. (Pubitemid 350076515)
20. Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR. 2009. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324: 407-410.
21. Miller JC, Holmes MC, Wang J, Guschin DY, Lee YL, Rupniewski I, Beausejour CM, Waite AJ, Wang NS, Kim KA, et al. 2007. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25: 778-785. (Pubitemid 47052191)
22. Moehle EA, Rock JM, Lee YL, Jouvenot Y, Dekelver RC, Gregory PD, Urnov FD, Holmes MC. 2007. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci 104: 3055-3060. (Pubitemid 46364112)
23. Mulder J, Ariaens A, van den Boomen D, Moolenaar WH. 2004. p116Rip targets myosin phosphatase to the actin cytoskeleton and is essential for RhoA/ROCK-regulated neuritogenesis. Mol Biol Cell 15: 5516-5527.
24. Orlando S, Santiago Y, Dekelver RC, Freyvert Y, Boydston EA, Moehle EA, Choi VM, Gopalan SML, Li JF, Miller J, et al. 2010. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res (in press). doi: 10.1093/nar/gkq512.
25. Osborne EA, Dudoit S, Rine J. 2009. The establishment of gene silencing at single-cell resolution. Nat Genet 41: 800-806.
26. Paddison P, Silva J, Conklin D, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, et al. 2004. A resource for large-scale RNA-interference-based screens in mammals. Natured 428: 427-431.
27. + T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26: 808-816.
28. Rebar EJ, Pabo CO. 1994. Zinc finger phage: Affinity selection of fingers with new DNA-binding specificities. Science 263: 671-673.
29. Richardson C, Jasin M. 2000. Coupled homologous and nonhomologous repair of a double-strand break preserves genomic integrity in mammalian cells. Mol Cell Biol 20: 9068-9075. (Pubitemid 32245935)
30. Rogatsky I, Trowbridge JM, Garabedian MJ. 1997. Glucocorticoid receptor-mediated cell cycle arrest is achieved through distinct cell-specific transcriptional regulatory mechanisms. Mol Cell Biol 17: 3181-3193. (Pubitemid 27215033)
31. Root DE, Hacohen N, Hahn WC, Lander ES, Sabatini DM. 2006. Genomescale loss-of-function screening with a lentiviral RNAi library. Nat Methods 3: 715-719. (Pubitemid 44275739)
32. Rouet P, Smih F, Jasin M. 1994. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14: 8096-8106. (Pubitemid 24373558)
33. Rubio MA, Kim SH, Campisi J. 2002. Reversible manipulation of telomerase expression and telomere length. Implications for the ionizing radiation response and replicative senescence of human cells. J Biol Chem 277: 28609-28617. (Pubitemid 41079289)
34. Ruis BL, Fattah KR, Hendrickson EA. 2008. The catalytic subunit of DNA-dependent protein kinase regulates proliferation, telomere length, and genomic stability in human somatic cells. Mol Cell Biol 28: 6182-6195.
35. Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM. 2008. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320: 1496-1501. (Pubitemid 351929429)
36. Sauer B, Henderson N. 1988. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1. Proc Natl Acad Sci 85: 5166-5170.
37. Sayegh R, Auerbach SD, Li X, Loftus RW, Husted RF, Stokes JB, Thomas CP. 1999. Glucocorticoid induction of epithelial sodium channel expression in lung and renal epithelia occurs via trans-activation of a hormone response element in the 59-flanking region of the human epithelial sodium channel alpha subunit gene. J Biol Chem 274: 12431-12437. (Pubitemid 129518007)
38. Smith JR, Maguire S, Davis LA, Alexander M, Yang F, Chandran S, ffrench-Constant C, Pedersen RA. 2008. Robust, persistent transgene expression in human embryonic stem cells is achieved with AAVS1-targeted integration. Stem Cells 26: 496-504.
39. Stallcup MR, Kim JH, Teyssier C, Lee YH, Ma H, Chen D. 2003. The roles of protein-protein interactions and protein methylation in transcriptional activation by nuclear receptors and their coactivators. J Steroid Biochem Mol Biol 85: 139-145. (Pubitemid 37011092)
40. Tan I, Ng CH, Lim L, Leung T. 2001. Phosphorylation of a novel myosin binding subunit of protein phosphatase 1 reveals a conserved mechanism in the regulation of actin cytoskeleton. J Biol Chem 276: 21209-21216. (Pubitemid 37413109)
41. Thomas KR, Folger KR, Capecchi MR. 1986. High frequency targeting of genes to specific sites in the mammalian genome. Cell 44: 419-428. (Pubitemid 16043333)
42. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646-651. (Pubitemid 40825505)
43. Zambrowicz BP, Imamoto A, Fiering S, Herzenberg LA, Kerr WG, Soriano P. 1997. Disruption of overlapping transcripts in the ROSA beta geo 26 gene trap strain leads to widespread expression of beta-galactosidase in mouse embryos and hematopoietic cells. Proc Natl Acad Sci 94: 3789-3794. (Pubitemid 27180451)
44. Zaret KS, Yamamoto KR. 1984. Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element. Cell 38: 29-38.