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. 1994 Sep;68(9):5439–5447. doi: 10.1128/jvi.68.9.5439-5447.1994

Intramolecular recombination in polyomavirus DNA is a nonconservative process directed from the viral intergenic region.

C Nault 1, A Fricker 1, L Delbecchi 1, D Bourgaux-Ramoisy 1, P Bourgaux 1
PMCID: PMC236944  PMID: 8057426

Abstract

Previously, we have studied intramolecular homologous recombination in polyomavirus replicons under conditions allowing only one amplifiable recombination product to be generated from a single precursor molecule. In order to detect putative reciprocal product(s), we have now constructed precursor polyomavirus replicons which contain two copies, instead of one copy, of the viral intergenic region, including the origin of replication as well as both promoters. Upon transfection of mouse cells, constructs containing directly repeated intergenic regions yielded distinct amplifiable products, in number depending upon the functional integrity of both intergenic regions. Our data indicate that of two possible reciprocal products, a given precursor molecule would yield either one or the other but never both at the same time. Most striking, however, is the observation that promoter function is required for recombination, while the origin of replication function may be needed only for amplification of the recombination product once it has been formed. The data reported here confirm and extend previous data suggesting that (i) transcription is instrumental in recombination between direct repeats and (ii) nonconservative recombination involving direct repeats relies upon two promoters of opposing polarities.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alessandrini A., Desiderio S. V. Coordination of immunoglobulin DJH transcription and D-to-JH rearrangement by promoter-enhancer approximation. Mol Cell Biol. 1991 Apr;11(4):2096–2107. doi: 10.1128/mcb.11.4.2096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Anderson R. A., Eliason S. L. Recombination of homologous DNA fragments transfected into mammalian cells occurs predominantly by terminal pairing. Mol Cell Biol. 1986 Sep;6(9):3246–3252. doi: 10.1128/mcb.6.9.3246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bourgaux P., Gendron D., Bourgaux-Ramoisy D. Preferred crossover sites on polyomavirus DNA. J Virol. 1990 May;64(5):2327–2336. doi: 10.1128/jvi.64.5.2327-2336.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bourgaux P., Sylla B. S., Chartrand P. Excision of polyoma virus DNA from that of a transformed mouse cell: identification of a hybrid molecule with direct and inverted repeat sequences at the viral-cellular joints. Virology. 1982 Oct 15;122(1):84–97. doi: 10.1016/0042-6822(82)90379-8. [DOI] [PubMed] [Google Scholar]
  5. Brouillette S., Chartrand P. Intermolecular recombination assay for mammalian cells that produces recombinants carrying both homologous and nonhomologous junctions. Mol Cell Biol. 1987 Jun;7(6):2248–2255. doi: 10.1128/mcb.7.6.2248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chakrabarti S., Seidman M. M. Intramolecular recombination between transfected repeated sequences in mammalian cells is nonconservative. Mol Cell Biol. 1986 Jul;6(7):2520–2526. doi: 10.1128/mcb.6.7.2520. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Frappier D., Gendron D., Bourgaux-Ramoisy D., Bourgaux P. Alternative homologous and nonhomologous products arising from intramolecular recombination. J Virol. 1990 Oct;64(10):5058–5065. doi: 10.1128/jvi.64.10.5058-5065.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fried M., Griffin B. E., Lund E., Robberson D. L. Polyoma virus--a study of wild-type, mutant and defective DNAs. Cold Spring Harb Symp Quant Biol. 1975;39(Pt 1):45–52. doi: 10.1101/sqb.1974.039.01.009. [DOI] [PubMed] [Google Scholar]
  9. Giaever G. N., Wang J. C. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell. 1988 Dec 2;55(5):849–856. doi: 10.1016/0092-8674(88)90140-7. [DOI] [PubMed] [Google Scholar]
  10. Gélinas C., Bouchard L., Bastin M. Tumorigenic activity of cloned polyoma virus DNA in newborn rats. Experientia. 1981 Oct 15;37(10):1074–1075. doi: 10.1007/BF02085017. [DOI] [PubMed] [Google Scholar]
  11. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  12. Harland R. M., Weintraub H., McKnight S. L. Transcription of DNA injected into Xenopus oocytes is influenced by template topology. Nature. 1983 Mar 3;302(5903):38–43. doi: 10.1038/302038a0. [DOI] [PubMed] [Google Scholar]
  13. Hendrickson E. A., Fritze C. E., Folk W. R., DePamphilis M. L. The origin of bidirectional DNA replication in polyoma virus. EMBO J. 1987 Jul;6(7):2011–2018. doi: 10.1002/j.1460-2075.1987.tb02465.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol. 1967 Jun 14;26(2):365–369. doi: 10.1016/0022-2836(67)90307-5. [DOI] [PubMed] [Google Scholar]
  15. Hsieh P., Camerini-Otero R. D. Formation of joint DNA molecules by two eukaryotic strand exchange proteins does not require melting of a DNA duplex. J Biol Chem. 1989 Mar 25;264(9):5089–5097. [PubMed] [Google Scholar]
  16. Ikeda H., Matsumoto T. Transcription promotes recA-independent recombination mediated by DNA-dependent RNA polymerase in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4571–4575. doi: 10.1073/pnas.76.9.4571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lee M. S., Garrard W. T. Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9675–9679. doi: 10.1073/pnas.88.21.9675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Leung H., Maizels N. Transcriptional regulatory elements stimulate recombination in extrachromosomal substrates carrying immunoglobulin switch-region sequences. Proc Natl Acad Sci U S A. 1992 May 1;89(9):4154–4158. doi: 10.1073/pnas.89.9.4154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lin F. L., Sperle K. M., Sternberg N. L. Extrachromosomal recombination in mammalian cells as studied with single- and double-stranded DNA substrates. Mol Cell Biol. 1987 Jan;7(1):129–140. doi: 10.1128/mcb.7.1.129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lin F. L., Sperle K., Sternberg N. Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products. Mol Cell Biol. 1990 Jan;10(1):103–112. doi: 10.1128/mcb.10.1.103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lin F. L., Sperle K., Sternberg N. Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process. Mol Cell Biol. 1984 Jun;4(6):1020–1034. doi: 10.1128/mcb.4.6.1020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027. doi: 10.1073/pnas.84.20.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Luchnik A. N., Hisamutdinov T. A., Georgiev G. P. Inhibition of transcription in eukaryotic cells by X-irradiation: relation to the loss of topological constraint in closed DNA loops. Nucleic Acids Res. 1988 Jun 10;16(11):5175–5190. doi: 10.1093/nar/16.11.5175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Luthman H., Nilsson M. G., Magnusson G. Non-contiguous segments of the polyoma genome required in cis for DNA replication. J Mol Biol. 1982 Nov 15;161(4):533–550. doi: 10.1016/0022-2836(82)90406-5. [DOI] [PubMed] [Google Scholar]
  25. Nault C., Veilleux S., Delbecchi L., Bourgaux-Ramoisy D., Bourgaux P. Intramolecular recombination in polyomavirus DNA is controlled by promoter elements. Nucleic Acids Res. 1994 Feb 11;22(3):485–491. doi: 10.1093/nar/22.3.485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nickoloff J. A., Reynolds R. J. Transcription stimulates homologous recombination in mammalian cells. Mol Cell Biol. 1990 Sep;10(9):4837–4845. doi: 10.1128/mcb.10.9.4837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Piché A., Bourgaux P. Resolution of a polyomavirus-mouse hybrid replicon: release of genomic viral DNA. J Virol. 1987 Mar;61(3):840–844. doi: 10.1128/jvi.61.3.840-844.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Piché A., Bourgaux P. Resolution of a polyomavirus-mouse hybrid replicon: viral function required for recombination. J Virol. 1987 Mar;61(3):845–850. doi: 10.1128/jvi.61.3.845-850.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rautmann G., Glaichenhaus N., Nahgashfar Z., Breathnach R., Rassoulzadegan M. Complementation of a tsa mutant and replication of a recombinant DNA carrying the viral ori region in mouse cells transformed by polyoma virus. Virology. 1982 Oct 30;122(2):306–317. doi: 10.1016/0042-6822(82)90230-6. [DOI] [PubMed] [Google Scholar]
  30. Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. doi: 10.1126/science.2999980. [DOI] [PubMed] [Google Scholar]
  31. Schlissel M. S., Baltimore D. Activation of immunoglobulin kappa gene rearrangement correlates with induction of germline kappa gene transcription. Cell. 1989 Sep 8;58(5):1001–1007. doi: 10.1016/0092-8674(89)90951-3. [DOI] [PubMed] [Google Scholar]
  32. Seidman M. M. Intermolecular homologous recombination between transfected sequences in mammalian cells is primarily nonconservative. Mol Cell Biol. 1987 Oct;7(10):3561–3565. doi: 10.1128/mcb.7.10.3561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  34. Stewart S. E., Roeder G. S. Transcription by RNA polymerase I stimulates mitotic recombination in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Aug;9(8):3464–3472. doi: 10.1128/mcb.9.8.3464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sussman D. J., Milman G. Short-term, high-efficiency expression of transfected DNA. Mol Cell Biol. 1984 Aug;4(8):1641–1643. doi: 10.1128/mcb.4.8.1641. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sylla B. S., Allard D., Roy G., Bourgaux-Ramoisy D., Bourgaux P. A mouse DNA sequence that mediates integration and excision of polyoma virus DNA. Gene. 1984 Sep;29(3):343–350. doi: 10.1016/0378-1119(84)90063-5. [DOI] [PubMed] [Google Scholar]
  37. Sylla B. S., Huberdeau D., Bourgaux-Ramoisy D., Bourgaux P. Site-specific excision of integrated polyoma DNA. Cell. 1984 Jun;37(2):661–667. doi: 10.1016/0092-8674(84)90398-2. [DOI] [PubMed] [Google Scholar]
  38. Thomas B. J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 1989 Feb 24;56(4):619–630. doi: 10.1016/0092-8674(89)90584-9. [DOI] [PubMed] [Google Scholar]
  39. Voelkel-Meiman K., Keil R. L., Roeder G. S. Recombination-stimulating sequences in yeast ribosomal DNA correspond to sequences regulating transcription by RNA polymerase I. Cell. 1987 Mar 27;48(6):1071–1079. doi: 10.1016/0092-8674(87)90714-8. [DOI] [PubMed] [Google Scholar]
  40. Vu H. K., Delbecchi L., Bourgaux-Ramoisy D., Bourgaux P. The same mammalian replicon yields distinct recombination products in different cell lines. J Biol Chem. 1991 May 15;266(14):9320–9326. [PubMed] [Google Scholar]
  41. Vu H. K., Delbecchi L., Quévillon M., Herring-Gillam E., Bourgaux P. Crossover site selection during recombination of polyomavirus replicons. J Virol. 1992 May;66(5):3210–3213. doi: 10.1128/jvi.66.5.3210-3213.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wake C. T., Vernaleone F., Wilson J. H. Topological requirements for homologous recombination among DNA molecules transfected into mammalian cells. Mol Cell Biol. 1985 Aug;5(8):2080–2089. doi: 10.1128/mcb.5.8.2080. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Waldman A. S., Liskay R. M. Differential effects of base-pair mismatch on intrachromosomal versus extrachromosomal recombination in mouse cells. Proc Natl Acad Sci U S A. 1987 Aug;84(15):5340–5344. doi: 10.1073/pnas.84.15.5340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Weintraub H., Cheng P. F., Conrad K. Expression of transfected DNA depends on DNA topology. Cell. 1986 Jul 4;46(1):115–122. doi: 10.1016/0092-8674(86)90865-2. [DOI] [PubMed] [Google Scholar]
  45. Wu H. Y., Shyy S. H., Wang J. C., Liu L. F. Transcription generates positively and negatively supercoiled domains in the template. Cell. 1988 May 6;53(3):433–440. doi: 10.1016/0092-8674(88)90163-8. [DOI] [PubMed] [Google Scholar]

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