Small fragment homologous replacement (SFHR): Sequence-specific modification of genomic DNA in eukaryotic cells by small DNA fragments

Methods in Molecular Biology

Volumn 1114, Issue , 2014, Pages 85-101

  Luchetti, Andrea ^a   Malgieri, Arianna ^a   Sangiuolo, Federica ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

Cell cycle; Gene targeting; Homologous replacement; Small DNA fragments (SDF); Small fragment homologous replacement (SFHR)

Indexed keywords

DNA; DNA FRAGMENT; GENOMIC DNA; RNA; COMPLEMENTARY DNA; MESSENGER RNA; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1;

ALLELE; ARTICLE; CELL CULTURE; CELL CYCLE; DNA EXTRACTION; DNA MODIFICATION; DNA SEQUENCE; ENHANCER REGION; ENZYME ANALYSIS; EUKARYOTIC CELL; FIBROBLAST; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENE THERAPY; GENETIC DISORDER; GENOTYPE; HUMAN; NONHUMAN; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROMOTER REGION; PURIFICATION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA EXTRACTION; SIMIAN VIRUS 40; SMALL FRAGMENT HOMOLOGOUS REPLACEMENT; SOUTHERN BLOTTING; SPINAL MUSCULAR ATROPHY; AMPLICON; ANALYSIS; ANIMAL CELL; CELL SYNCHRONIZATION; CHEMICAL MODIFICATION; CONTROLLED STUDY; EMBRYO; HOMOLOGOUS RECOMBINATION; MOUSE; RESTRICTION SITE;

EUKARYOTA; MURINAE;

ANIMALS; CELL CULTURE TECHNIQUES; CELL CYCLE; DNA; EUKARYOTIC CELLS; FLOW CYTOMETRY; GENE EXPRESSION; GENE TARGETING; GENOTYPING TECHNIQUES; HOMOLOGOUS RECOMBINATION; HUMANS; MICE; SEQUENCE ANALYSIS, DNA; TRANSFECTION;

EID: 84922014050     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-761-7_6     Document Type: Article

References (32)

1. Capecchi MR (1994) Targeted gene replacement. Sci Am 270:52-59
2. Sullenger B (2003) Targeted genetic repair: an emerging approach to genetic therapy. J Clin Invest 112:310-311
3. Horie K, Kuroiwa A, Ikawa M, Okabe M, Kondoh G, Matsuda Y, Takeda J (2001) Efficient chromosomal transposition of a Tc1/marinerlike transposon Sleeping Beauty in mice. Proc Natl Acad Sci USA 98:9191-9196
4. Ivics Z, Plasterk RH, Izsvak Z (1997) Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91(4):501-510
5. Izsvak Z (2003) Sleeping beauty transposition: biology and applications for molecular therapy. Mol Ther 9(2):147-156
6. Yoon K, Cole-Strauss A, Kmiec EB (1996) Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA-DNA oligonucleotide. Proc Natl Acad Sci USA 93:2017-2076
7. Zhu T, Mettenburg K, Peterson DJ, Tagliani L, Baszczynski CL (2000) Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides. Nat Biotechnol 18:555-558
8. McManus MT, Sharp PA (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3(10):737-747
9. 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(7042):646-651
10. Gruenert DC (1998) Gene correction with small DNA fragments. Curr Res Mol Therapeut 1:607-613
11. Gruenert DC (1999) Opportunities and challenges in targeting genes for therapy. Gene Ther 6:1347-1348
12. Y?ez RJ, Porter AC (1998) Therapeutic gene targeting. Gene Ther 5(2):149-159
13. Goncz KK, Gruenert DC (2000) Site-directed alteration of genomic DNA by small-fragment homologous replacement. Methods Mol Biol 133:85-99
14. Davis BR, Gruenert DC (2002) Application of SFHR to gene therapy of monogenic disorders. Gene Ther 9:691-694
15. Kunzelmann K, Legendre JY, Knoell DL, Escobar LC, Xu Z, Gruenert DC (1996) Gene targeting of CFTR DNA in CF epithelial cells. Gene Ther 3:859-867
16. Colosimo A, Goncz KK, Novelli G, Dallapiccola B, Gruenert DC (2001) Targeted correction of a defective selectable marker gene in human epithelial cells by small DNA fragments. Mol Ther 3:178-185
17. Sangiuolo F, Bruscia E, Serafino A, Nardone AM, Bonifazi E, Lais M, Gruenert DC, Novelli G (2002) In vitro correction of cystic fibrosis epithelial cell lines by small fragment homologous replacement (SFHR) technique. BMC Med Genet 3:8
18. Maurisse R, Cheung J, Widdicombe J, Gruenert DC (2006) Modification of the pig CFTR gene mediated by small fragment homologous replacement. Ann N Y Acad Sci 1082:120-123
19. Sangiuolo F, Scaldaferri ML, Filareto A, Spitalieri P, Guerra L et al (2008) Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR). Front Biosci 1:2989-2999
20. Quigley A, Lynch GS, Steeper K, Kornberg AJ, Gregorevic P, Austin L, Byrne E (2001) In vivo and in vitro correction of the mdx dystrophin gene nonsense mutation by short-fragment homologous replacement. Hum Gene Ther 12:629-642
21. Todaro M, Quigley A, Kita M, Chin J, Lowes K, Kornberg AJ, Cook MJ, Kapsa R (2007) Effective detection of corrected dystrophin loci in mdx mouse myogenic precursors. Hum Mutat 28:816-823
22. Sangiuolo F, Filareto A, Spitalieri P, Scaldaferri ML, Mango R et al (2005) In vitro restoration of functional SMN protein in human trophoblast cells affected by spinal muscular atrophy by small fragment homologous replacement. Hum Gene Ther 16:869-880
23. Spitalieri P, Cortese G, Pietropolli A, Filareto A, Dolci S et al (2009) Identification of multipotent cytotrophoblast cells from human first trimester chorionic villi. Cloning Stem Cells 11:535-546
24. Zayed H, McIvor RS, Wiest DL, Blazar BR (2006) In vitro functional correction of the mutation responsible for murine severe combined immune deficiency by small fragment homologous replacement. Hum Gene Ther 17:158-166
25. Goncz KK, Prokopishyn NL, Abdolmohammadi A, Bedayat B, Maurisse R, Davis BR, Gruenert DC (2006) Small fragment homologous replacement-mediated modification of genomic beta-globin sequences in human hematopoietic stem/progenitor cells. Oligonucleotides 16: 213-224
26. Bedayat B, Abdolmohamadi A, Ye L, Maurisse R, Parsi H et al (2009) Sequence-specific correction of genomic hypoxanthine-guanine phosphoribosyl transferase mutations in lymphoblasts by small fragment homologous replacement. Oligonucleotides 20:7-16
27. Hu Y, Parekh-Olmedo H, Drury M, Skogen M, Kmiec EB (2005) Reaction parameters of targeted gene repair in mammalian cells. Mol Biotechnol 29:197-210
28. Engstrom JU, Kmiec EB (2008) DNA replication, cell cycle progression and the targeted gene repair reaction. Cell Cycle 7:1402-1414
29. Brachman EE, Kmiec EB (2005) Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks. DNA Repair 4:445-457
30. Gruenert DC, Bruscia E, Novelli G, Colosimo A, Dallapiccola B et al (2003) Sequence-specific modification of genomic DNA by small DNA fragments. J Clin Invest 112:637-641
31. Luchetti A, Filareto A, Sanchez M, Ferraguti G, Lucarelli M, Novelli G, Sangiuolo F, Malgieri A (2012) Small fragment homologous replacement: evaluation of factors influencing modification efficiency in an eukaryotic assay system. PLoS One 7(2):e30851
32. Maurisse R, Fichou Y, De Semir D, Cheung J, Ferec C, Gruenert DC (2006) Gel purification of genomic DNA removes contaminating small DNA fragments interfering with PCR analysis of SFHR. Oligonucleotides 16:375-386