Abstract
Foreign DNA integration is one of the most widely exploited cellular processes in molecular biology. Its technical use permits us to alter a cellular genome by incorporating a fragment of foreign DNA into the chromosomal DNA. This process employs the cell's own endogenous DNA modification and repair machinery. Two main classes of integration mechanisms exist: those that draw on sequence similarity between the foreign and genomic sequences to carry out homology-directed modifications, and the nonhomologous or ‘illegitimate’ insertion of foreign DNA into the genome. Gene therapy procedures can result in illegitimate integration of introduced sequences and thus pose a risk of unforeseeable genomic alterations. The choice of insertion site, the degree to which the foreign DNA and endogenous locus are modified before or during integration, and the resulting impact on structure, expression, and stability of the genome are all factors of illegitimate DNA integration that must be considered, in particular when designing genetic therapies.
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References
Colosimo A et al. Transfer and expression of foreign genes in mammalian cells. Biotechniques 2000; 29: 314–318.
Salman H et al. Kinetics and mechanism of DNA uptake into the cell nucleus. Proc Natl Acad Sci USA 2001; 98: 7247–7252.
Liang F, Jasin M . Ku80-deficient cells exhibit excess degradation of extrachromosomal DNA. J Biol Chem 1996; 271: 14405–14411.
Jenke BHC et al. An episomally replicating vector binds to the nuclear matrix protein SAF-A in vivo. EMBO Rep 2002; 3: 349–354.
Gorman C, Padmanabhan R, Howard BH . High efficiency DNA-mediated transformation of primate cells. Science 1983; 221: 551–553.
Staunton JE, Weaver DT . Scid cells efficiently integrate hairpin and linear DNA substrates. Mol Cell Biol 1994; 14: 3876–3883.
Bergsmedh A et al. Horizontal transfer of oncogenes by uptake of apoptotic bodies. Proc Natl Acad Sci USA 2001; 98: 6407–6411.
Willett-Brozick JE, Savul SA, Richey LE, Baysal BE . Germline insertion of mtDNA at the breakpoint junction of a reciprocal constitutional translocation. Hum Genet 2001; 109: 216–223.
Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology: Washington, DC, 1989.
Esnault C, Maestre J, Heidmann T . Human LINE retrotransposons generate processed pseudogenes. Nat Genet 2000; 24: 363–367.
Vasquez KM, Marburger K, Intody Z, Wilson JH . Manipulating the mammalian genome by homologous recombination. Proc Natl Acad Sci USA 2001; 98: 8403–8410.
Goncz KK et al. Application of SFHR to gene therapy of monogenic disorders. Gene Therapy 2002; 9: 691–6944.
Babinet C, Cohen-Tannoudji M . Genome engineering via homologous recombination in mouse embryonic stem (ES) cells: an amazingly versatile tool for the study of mammalian biology. An Acad Bras Cienc 2001; 73: 365–383.
Smith K . Theoretical mechanisms in targeted and random integration of transgene DNA. Reprod Nutr Dev 2001; 41: 465–485.
Takata M et al. Homologous recombination and non-homologous end-joining pathways of DNA double-strand break repair have overlapping roles in the maintenance of chromosomal integrity in vertebrate cells. EMBO J 1998; 17: 5497–5508.
Ledwith BJ et al. Plasmid DNA vaccines: investigation of integration into host cellular DNA following intramuscular injection in mice. Intervirology 2000; 43: 258–272.
Manam S et al. Plasmid DNA vaccines: tissue distribution and effects of DNA sequence, adjuvants and delivery method on integration into host DNA. Intervirology 2000; 43: 273–281.
Taganov K et al. Characterization of retrovirus–host DNA junctions in cells deficient in non-homologous-end joining. J Virol 2001; 75: 9549–9552.
Holmes-Son ML, Appa RS, Chow SA . Molecular genetics and target site specificity of retroviral integration. Adv Genet 2001; 43: 33–69.
Hindmarsh P, Leis J . Retroviral DNA integration. Microbiol Mol Biol Rev 1999; 63: 836–843.
Belmaaza A, Chartrand P . One-sided invasion events in homologous recombination at double-strand breaks. Mutat Res 1994; 314: 199–208.
van den Bosch M, Lohman PH, Pastink A . DNA double-strand break repair by homologous recombination. Biol Chem 2002; 383: 873–892.
Lin FL, Sperle K, Sternberg NL . Repair of double-stranded DNA breaks by homologous DNA fragments during transfer of DNA into mouse L cells. Mol Cell Biol 1990; 10: 113–119.
Lin FL, Sperle KM, Sternberg NL . Extrachromosomal recombination in mammalian cells as studied with single and double-stranded DNA substrates. Mol Cell Biol 1987; 7: 129–140.
Folger KR, Thomas K, Capecchi MR . Nonreciprocal exchanges of information between DNA duplexes coinjected into mammalian cell nuclei. Mol Cell Biol 1985; 5: 59–69.
Subramani S, Rubnitz J . Recombination events after transient infection and stable integration of DNA into mouse cells. Mol Cell Biol 1985; 5: 659–666.
Tremblay A, Jasin M, Chartrand P . A double-strand break in a chromosomal LINE element can be repaired by gene conversion with various endogenous LINE elements in mouse cells. Mol Cell Biol 2000; 20: 54–60.
Richardson C, Jasin M . Coupled homologous and nonhomologous repair of a double-strand break preserves genomic integrity in mammalian cells. Mol Cell Biol 2000; 20: 9068–9075.
Dellaire G et al. Evidence that extrachromosomal double-strand break repair can be coupled to the repair of chromosomal double-strand breaks in mammalian cells. Chromosoma 2002; 111: 304–312.
Wong EA, Capecchi MR . Analysis of homologous recombination in cultured mammalian cells in transient expression and stable transformation assays. Somat Cell Mol Genet 1986; 12: 63–72.
Wong EA, Capecchi MR . Homologous recombination between coinjected DNA sequences peaks in early to mid-S phase. Mol Cell Biol 1987; 7: 2294–2295.
Calos MP, Lebkowski JS, Botchan MR . High mutation frequency in DNA transfected into mammalian cells. Proc Natl Acad Sci USA 1983; 80: 3015–3019.
Wilson JH, Berget PB, Pipas JM . Somatic cells efficiently join unrelated DNA segments end-to-end. Mol Cell Biol 1982; 2: 1258–1269.
Wake CT et al. How damaged is the biologically active subpopulation of transfected DNA. Mol Cell Biol 1984; 4: 387–398.
Burdon TG, Wall RJ . Fate of microinjected genes in preimplantation mouse embryo. Mol Reprod Dev 1992; 33: 436–442.
Roth DB, Wilson JH . Nonhomologous recombination in mammalian cells: role for sequence homologies in the joining reaction. Mol Cell Biol 1986; 6: 4295–4304.
Nicolas AL, Young CSH . Characterization of DNA end joining in a mammalian cell nuclear extract: junction formation is accompanied by nucleotide loss, which is limited and uniform but not site specific. Mol Cell Biol 1994; 14: 170–180.
Critchlow SE, Jackson SP . DNA end-joining: from yeast to man. TIBS 1998; 23: 394–398.
Perucho M, Hanahan D, Wigler M . Genetic and physical linkage of exogenous sequences in transformed cells. Cell 1980; 22: 309–317.
Gordon et al. Genetic transformation of mouse embryos by microinjection of purified DNA. Proc Natl Acad Sci USA 1980; 77: 7380–7384.
Folger KR, Wong EA, Wahl G, Capecchi MR . Patterns of integration of DNA microinjected into cultured mammalian cells: evidence for homologous recombination between injected plasmid DNA molecules. Mol Cell Biol 1982; 2: 1372–1387.
Chen C, Chasin LA . Cointegration of DNA molecules introduced into mammalian cells by electroporation. Somat Cell Mol Genet 1998; 24: 249–256.
Hamada T, Sasaki H, Seki R, Sakaki Y . Mechanism of chromosomal integration of transgenes in microinjected mouse eggs: sequence analysis of genome–transgene and transgene–transgene junctions at two loci. Gene 1993; 128: 197–202.
McFarlane M, Wilson JB . A model for the mechanism of precise integration of a microinjected transgene. Transgenic Res 1996; 5: 171–177.
Robins DM, Ripley S, Henderson AS, Axel R . Transforming DNA integrates into the host chromosome. Cell 1981; 23: 29–39.
Merrihew R et al. High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome. Mol Cell Biol 1996; 16: 10–18.
Merrihew RV et al. Chromosomal integration of transduced recombinant baculovirus DNA in mammalian cells. J Virol 2001; 75: 903–909.
Hoglund M, Siden T, Rohme D . Different pathways for chromosomal integration of transfected circular pSVneo plasmids in normal and established rodent cells. Gene 1992; 116: 215–222.
Botchan M, Stringer J, Mitchison T, Sambrook J . Integration and excision of SV40 DNA from the chromosome of a transformed cell. Cell 1980; 20: 143–152.
Covarrubias L, Nishida Y, Mintz B . Early postimplantation embryo lethality due to DNA rearrangements in a transgenic mouse strain. Proc Natl Acad Sci USA 1986; 83: 6020–6024.
Covarrubias L et al. Cellular DNA rearrangements and early developmental arrest caused by DNA insertion in transgenic mouse embryos. Mol Cell Biol 1987; 7: 2243–2247.
Mark WH et al. Genomic structure of the locus associated with an insertional mutation in line 4 transgenic mice. Genomics 1992; 13: 159–166.
Colbère-Garapin F et al. Patterns of integration of exogenous DNA sequences transfected into mammalian cells of primate and rodent origin. Gene 1986; 50: 279–288.
Lohrer H, Blum M, Herrlich P . Ataxia telangiestasia resists gene cloning: an account of parameters determining gene transfer into human recipient cells. Mol Gen Genet 1988; 212: 474–480.
Hoeijmakers JH, Odijk H, Westerveld A . Differences between rodent and human cell lines in the amount of integrated DNA after transfection. Exp Cell Res 1987; 169: 111–119.
Mayne LV et al. SV-40-transformed normal and DNA repair deficient human fibroblasts can be transfected with high frequency but retain only limited amount of integrated DNA. Gene 1988; 66: 65–76.
Toneguzzo F, Keating A, Glynn S, McDonald K . Electric field-mediated gene transfer: characterization of DNA transfer and patterns of integration in lymphoid cells. Nucleic Acids Res 1988; 16: 5515–5532.
Kato S, Anderson RA, Camerini-Otero RD . Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome. Mol Cell Biol 1986; 6: 1787–1795.
Wilkie TM, Palmiter RD . Analysis of the integrant in MyK-103 transgenic mice in which males fail to transmit the integrant. Mol Cell Biol 1987; 7: 1646–1655.
Mahon KA, Overbeek PA, Westphal H . Prenatal lethality in a transgenic mouse line is the result of a chromosomal translocation. Proc Natl Acad Sci USA 1988; 85: 1165–1168.
Rijkers T, Peetz A, Ruther U . Insertional mutagenesis in transgenic mice. Transgenic Res 1994; 3: 203–215.
Lander ES et al. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860–921.
Murnane JP, Yu LC . Acquisition of telomere repeat sequences by transfected DNA integrated at the site of a chromosome break. Mol Cell Biol 1993; 13: 977–983.
Farr C, Fantes J, Goodfellow P, Cooke H . Functional reintroduction of human telomeres into mammalian cells. Proc Natl Acad Sci USA 1991; 88: 7006–7010.
Heller H, Kammer C, Wilgenbus P, Doerfler W . Chromosomal insertion of foreign (adenovirus type 12, plasmid, or bacteriophage A) DNA is associated with enhanced methylation of cellular DNA segments. Proc Natl Acad Sci USA 1995; 92: 5515–5519.
Remus R et al. Insertion of foreign DNA into an established mammalian genome can alter the methylation of cellular DNA sequences. J Virol 1999; 73: 1010–1022.
Bestor TH . The host defence function of genomic methylation patterns. Novartis Found Symp 1998; 214: 187–195.
Garrick D et al. Repeat-induced gene silencing in mammals. Nat Genet 1998; 18: 56–59.
McBurney MW et al. Evidence for repeat-induced gene silencing in cultured mammalian cells: inactivation of tandem repeats of transfected genes. Exp Cell Res 2002; 274: 1–8.
Migliaccio AR et al. Stable and unstable transgene integration sites in the human genome: extinction of the green fluorescent protein transgene in K562 cells. Gene 2000; 256: 197–214.
Sager R, Anisowicz A, Howell N . Genomic rearrangements in a mouse cell line containing integrated SV40 DNA. Cell 1981; 23: 41–50.
Mounts P, Kelly TJ . Rearrangements of host and viral DNA in mouse cells transformed by simian virus 40. J Mol Biol 1984; 177: 431–460.
Bender MA, Brockman WW . Rearrangement of integrated viral DNA sequences in mouse cells transformed by simian virus 40. J Virol 1981; 38: 872–879.
Weidle UH et al. Amplified expression constructs for human tissue-type plasminogen activator in Chinese hamster ovary cells: instability in the absence of selective pressure. Gene 1988; 66: 193–203.
McBurney MW et al. Reexpression of a cluster of silenced transgenes is associated with their rearrangement. Gene Chromosome Cancer 2001; 32: 311–323.
Milot E et al. Chromosomal illegitimate recombination in mammalian cells is associated with intrinsically bent DNA elements. EMBO J 1992; 11: 5063–5070.
Kusakabe T et al. Linearization and integration of DNA into cells preferentially occurs at intrinsically curved regions from human LINE-1 repetitive element. Gene 2001; 274: 271–281.
Heartlein MW, Knoll JH, Latt SA . Chromosome instability associated with human alphoid DNA transfected into the Chinese hamster genome. Mol Cell Biol 1988; 8: 3611–3618.
Kaufman RJ, Sharp PA, Latt SA . Evolution of chromosomal regions containing transfected and amplified dihydrofolate reductase sequences. Mol Cell Biol 1983; 3: 699–711.
Wahl GM, Robert de Saint Vincent B, DeRose ML . Effect of chromosomal position on amplification of transfected genes in animal cells. Nature 1984; 307: 516–520.
Kilburn AE et al. Insertion of a telomere repeat sequence into a mammalian gene causes chromosome instability. Mol Cell Biol 2001; 21: 126–135.
Butner KA, Lo CW . High frequency DNA rearrangements associated with mouse centromeric satellite DNA. J Mol Biol 1986; 187: 547–556.
Rassool FV et al. Preferential integration of marker DNA into the chromosomal fragile site at 3p14: an approach to cloning fragile sites. Proc Natl Acad Sci USA 1991; 88: 6657–6661.
Rassool FV et al. Increased genetic instability of the common fragile site at 3p14 after integration of exogenous DNA. Am J Hum Genet 1992; 50: 1243–1251.
Bode J et al. Fatal connections: when DNA ends meet on the nuclear matrix. J Cell Biochem Suppl 2000; 35: 3–22.
Murnane JP . Inducible gene expression by DNA rearrangements in human cells. Mol Cell Biol 1986; 6: 549–558.
Murnane JP, Young BR . Nucleotide sequence analysis of novel junctions near an unstable integrated plasmid in human cells. Gene 1989; 84: 201–205.
Murnane JP . Influence of cellular sequences on instability of plasmid integration sites in human cells. Somat Cell Mol Genet 1990; 16: 195–209.
Dellaire G, Chartrand P . Direct evidence that transgene integration is random in murine cells, implying that naturally occurring double-strand breaks may be distributed similarly in the genome. Radiat Res 1998; 149: 325–329.
Sutherland HF, Lovell-Badge RH, Jackson IJ . Characterisation of two identical independent non-homologous integration sites in mouse embryonic stem cells. Gene 1993; 131: 265–268.
McCarthy S, Ward WS . Interaction of exogenous DNA with the nuclear matrix of live spermatozoa. Mol Reprod Dev 2000; 56: 235–237.
Magnano AR et al. Sperm/DNA interaction: integration of foreign DNA sequences in the mouse genome. J Reprod Immunol 1998; 41: 187–196.
Konopka AK . Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells. Nucleic Acids Res 1988; 16: 1739–1758.
Macleod D, Lovell-Badge R, Jones S, Jackson I . A promoter trap in embryonic stem cells selects for integration of DNA into CpG islands. Nucleic Acids Res 1991; 19: 17–23.
Chen CM, Choo KB, Cheng WT . Frequent deletions and sequence aberrations at the transgene junctions of transgenic mice carrying the papillomavirus regulatory and the SV40 TAg gene sequences. Transgenic Res 1995; 4: 52–59.
Rouet P, Smih F, Jasin M . Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc Natl Acad Sci USA 1994; 91: 6064–6068.
Vos JMH, Hanawalt PC . Effect of DNA damage on stable transformation of mammalian cells with integrative and episomal plasmids. Mutat Res 1989; 220: 205–220.
Reid LH, Shesely EG, Kim HS, Smithies O . Cotransformation and gene targeting in mouse embryonic stem cells. Mol Cell Biol 1991; 11: 2769–2777.
Scherbakova OG, Filatov MV . Camptothecin enhances random integration of transfected DNA into the genome of mammalian cells. Biochim Biophys Acta 2000; 1495: 1–3.
Manivasakam P, Aubrecht J, Sidhom S, Schiestl RH . Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells. Nucleic Acids Res 2001; 29: 4826–4833.
Fujimaki K et al. DNA Topoisomerase II inhibitors enhance random integration of transfected vectors into human chromosomes. Somat Cell Mol Genet 1996; 22: 279–290.
Bodley AL, Huang HC, Yu C, Liu LF . Integration of simian virus 40 into cellular DNA occurs at or near Topoisomerase II cleavage hotspots induced by VM-26 (teniposide). Mol Cell Biol 1993; 13: 6190–6200.
Spivak G, Ganesan AK, Hanawalt PC . Enhanced transformation of human cells by UV-irradiated pSV2 plasmids. Mol Cell Biol 1984; 4: 1169–1171.
van Hattikum H, Bunduck P, Hooykaas PJJ . Non-homologous end-joining proteins are required for Agrobacterium T-DNA integration. EMBO J 2001; 22: 6550–6558.
Zhong Q et al. BRCA1 facilitates microhomology-mediated end joining of DNA double strand breaks. J Biol Chem 2002; 277: 28641–28647.
Lin CT et al. Supression of gene amplification and chromosomal DNA integration by the DNA mismatch repair system. Nucleic Acids Res 2001; 29: 3304–3310.
Thyagarajan B, Johnson BL, Campbell C . The effect of target site transcription on gene targeting in human cells in vitro. Nucleic Acids Res 1995; 23: 2784–2790.
Lin Y, Waldman AS . Capture of DNA sequences at double-strand breaks in mammalian chromosomes. Genetics 2001; 158: 1665–1674.
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Würtele, H., Little, K. & Chartrand, P. Illegitimate DNA integration in mammalian cells. Gene Ther 10, 1791–1799 (2003). https://doi.org/10.1038/sj.gt.3302074
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DOI: https://doi.org/10.1038/sj.gt.3302074
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