Skip to main content
Genetics logoLink to Genetics
. 2003 Apr;163(4):1439–1447. doi: 10.1093/genetics/163.4.1439

Strand invasion and DNA synthesis from the two 3' ends of a double-strand break in Mammalian cells.

Richard D McCulloch 1, Leah R Read 1, Mark D Baker 1
PMCID: PMC1462519  PMID: 12702687

Abstract

Analysis of the crossover products recovered following transformation of mammalian cells with a sequence insertion ("ends-in") gene-targeting vector revealed a novel class of recombinant. In this class of recombinants, a single vector copy has integrated into an ectopic genomic position, leaving the structure of the cognate chromosomal locus unaltered. Thus, in this respect, the recombinants resemble simple cases of random vector integration. However, the important difference is that the two paired 3' vector ends have acquired endogenous, chromosomal sequences flanking both sides of the vector-borne double-strand break (DSB). In some cases, copying was extensive, extending >16 kb into nonhomologous flanking DNA. The results suggest that mammalian homologous recombination events can involve strand invasion and DNA synthesis by both 3' ends of the DSB. These DNA interactions are a central, predicted feature of the DSBR model of recombination.

Full Text

The Full Text of this article is available as a PDF (228.4 KB).

Selected References

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

  1. Adair G. M., Nairn R. S., Wilson J. H., Seidman M. M., Brotherman K. A., MacKinnon C., Scheerer J. B. Targeted homologous recombination at the endogenous adenine phosphoribosyltransferase locus in Chinese hamster cells. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4574–4578. doi: 10.1073/pnas.86.12.4574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Adair G. M., Scheerer J. B., Brotherman A., McConville S., Wilson J. H., Nairn R. S. Targeted recombination at the Chinese hamster APRT locus using insertion versus replacement vectors. Somat Cell Mol Genet. 1998 Mar;24(2):91–105. doi: 10.1023/b:scam.0000007112.62928.d8. [DOI] [PubMed] [Google Scholar]
  3. Allers T., Lichten M. Differential timing and control of noncrossover and crossover recombination during meiosis. Cell. 2001 Jul 13;106(1):47–57. doi: 10.1016/s0092-8674(01)00416-0. [DOI] [PubMed] [Google Scholar]
  4. Aratani Y., Okazaki R., Koyama H. End extension repair of introduced targeting vectors mediated by homologous recombination in mammalian cells. Nucleic Acids Res. 1992 Sep 25;20(18):4795–4801. doi: 10.1093/nar/20.18.4795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Baker M. D., Birmingham E. C. Evidence for biased holliday junction cleavage and mismatch repair directed by junction cuts during double-strand-break repair in mammalian cells. Mol Cell Biol. 2001 May;21(10):3425–3435. doi: 10.1128/MCB.21.10.3425-3435.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Baker M. D., Pennell N., Bosnoyan L., Shulman M. J. Homologous recombination can restore normal immunoglobulin production in a mutant hybridoma cell line. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6432–6436. doi: 10.1073/pnas.85.17.6432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Baumann B., Potash M. J., Köhler G. Consequences of frameshift mutations at the immunoglobulin heavy chain locus of the mouse. EMBO J. 1985 Feb;4(2):351–359. doi: 10.1002/j.1460-2075.1985.tb03636.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Belmaaza A., Chartrand P. One-sided invasion events in homologous recombination at double-strand breaks. Mutat Res. 1994 May;314(3):199–208. doi: 10.1016/0921-8777(94)90065-5. [DOI] [PubMed] [Google Scholar]
  9. Belmaaza A., Wallenburg J. C., Brouillette S., Gusew N., Chartrand P. Genetic exchange between endogenous and exogenous LINE-1 repetitive elements in mouse cells. Nucleic Acids Res. 1990 Nov 11;18(21):6385–6391. doi: 10.1093/nar/18.21.6385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cromie G. A., Connelly J. C., Leach D. R. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell. 2001 Dec;8(6):1163–1174. doi: 10.1016/s1097-2765(01)00419-1. [DOI] [PubMed] [Google Scholar]
  11. Cromie G. A., Leach D. R. Control of crossing over. Mol Cell. 2000 Oct;6(4):815–826. doi: 10.1016/s1097-2765(05)00095-x. [DOI] [PubMed] [Google Scholar]
  12. Donoho G., Jasin M., Berg P. Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol Cell Biol. 1998 Jul;18(7):4070–4078. doi: 10.1128/mcb.18.7.4070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Elliott B., Jasin M. Repair of double-strand breaks by homologous recombination in mismatch repair-defective mammalian cells. Mol Cell Biol. 2001 Apr;21(8):2671–2682. doi: 10.1128/MCB.21.8.2671-2682.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Elliott B., Richardson C., Winderbaum J., Nickoloff J. A., Jasin M. Gene conversion tracts from double-strand break repair in mammalian cells. Mol Cell Biol. 1998 Jan;18(1):93–101. doi: 10.1128/mcb.18.1.93. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ellis J., Bernstein A. Gene targeting with retroviral vectors: recombination by gene conversion into regions of nonhomology. Mol Cell Biol. 1989 Apr;9(4):1621–1627. doi: 10.1128/mcb.9.4.1621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Foss H. M., Hillers K. J., Stahl F. W. The conversion gradient at HIS4 of Saccharomyces cerevisiae. II. A role for mismatch repair directed by biased resolution of the recombinational intermediate. Genetics. 1999 Oct;153(2):573–583. doi: 10.1093/genetics/153.2.573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gilbertson L. A., Stahl F. W. A test of the double-strand break repair model for meiotic recombination in Saccharomyces cerevisiae. Genetics. 1996 Sep;144(1):27–41. doi: 10.1093/genetics/144.1.27. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gloor G. B., Nassif N. A., Johnson-Schlitz D. M., Preston C. R., Engels W. R. Targeted gene replacement in Drosophila via P element-induced gap repair. Science. 1991 Sep 6;253(5024):1110–1117. doi: 10.1126/science.1653452. [DOI] [PubMed] [Google Scholar]
  19. Gross-Bellard M., Oudet P., Chambon P. Isolation of high-molecular-weight DNA from mammalian cells. Eur J Biochem. 1973 Jul 2;36(1):32–38. doi: 10.1111/j.1432-1033.1973.tb02881.x. [DOI] [PubMed] [Google Scholar]
  20. Holmes A. M., Haber J. E. Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell. 1999 Feb 5;96(3):415–424. doi: 10.1016/s0092-8674(00)80554-1. [DOI] [PubMed] [Google Scholar]
  21. Hunter N., Kleckner N. The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination. Cell. 2001 Jul 13;106(1):59–70. doi: 10.1016/s0092-8674(01)00430-5. [DOI] [PubMed] [Google Scholar]
  22. Jasin M., Elledge S. J., Davis R. W., Berg P. Gene targeting at the human CD4 locus by epitope addition. Genes Dev. 1990 Feb;4(2):157–166. doi: 10.1101/gad.4.2.157. [DOI] [PubMed] [Google Scholar]
  23. Johnson R. D., Jasin M. Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells. EMBO J. 2000 Jul 3;19(13):3398–3407. doi: 10.1093/emboj/19.13.3398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Köhler G., Potash M. J., Lehrach H., Shulman M. J. Deletions in immunoglobulin mu chains. EMBO J. 1982;1(5):555–563. doi: 10.1002/j.1460-2075.1982.tb01208.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Li J., Baker M. D. Formation and repair of heteroduplex DNA on both sides of the double-strand break during mammalian gene targeting. J Mol Biol. 2000 Jan 21;295(3):505–516. doi: 10.1006/jmbi.1999.3400. [DOI] [PubMed] [Google Scholar]
  26. Malkova A., Ivanov E. L., Haber J. E. Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7131–7136. doi: 10.1073/pnas.93.14.7131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Morrow D. M., Connelly C., Hieter P. "Break copy" duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics. 1997 Oct;147(2):371–382. doi: 10.1093/genetics/147.2.371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ng P., Baker M. D. High efficiency site-specific modification of the chromosomal immunoglobulin locus by gene targeting. J Immunol Methods. 1998 May 1;214(1-2):81–96. doi: 10.1016/s0022-1759(98)00033-7. [DOI] [PubMed] [Google Scholar]
  29. Ng P., Baker M. D. Mechanisms of double-strand-break repair during gene targeting in mammalian cells. Genetics. 1999 Mar;151(3):1127–1141. doi: 10.1093/genetics/151.3.1127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Orr-Weaver T. L., Szostak J. W., Rothstein R. J. Yeast transformation: a model system for the study of recombination. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6354–6358. doi: 10.1073/pnas.78.10.6354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Pâques F., Haber J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1999 Jun;63(2):349–404. doi: 10.1128/mmbr.63.2.349-404.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pâques F., Leung W. Y., Haber J. E. Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol Cell Biol. 1998 Apr;18(4):2045–2054. doi: 10.1128/mcb.18.4.2045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Pâques F., Richard G. F., Haber J. E. Expansions and contractions in 36-bp minisatellites by gene conversion in yeast. Genetics. 2001 May;158(1):155–166. doi: 10.1093/genetics/158.1.155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Richardson C., Jasin M. Coupled homologous and nonhomologous repair of a double-strand break preserves genomic integrity in mammalian cells. Mol Cell Biol. 2000 Dec;20(23):9068–9075. doi: 10.1128/mcb.20.23.9068-9075.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sakagami K., Tokinaga Y., Yoshikura H., Kobayashi I. Homology-associated nonhomologous recombination in mammalian gene targeting. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8527–8531. doi: 10.1073/pnas.91.18.8527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Scheerer J. B., Adair G. M. Homology dependence of targeted recombination at the Chinese hamster APRT locus. Mol Cell Biol. 1994 Oct;14(10):6663–6673. doi: 10.1128/mcb.14.10.6663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Song K. Y., Schwartz F., Maeda N., Smithies O., Kucherlapati R. Accurate modification of a chromosomal plasmid by homologous recombination in human cells. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6820–6824. doi: 10.1073/pnas.84.19.6820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sun H., Treco D., Szostak J. W. Extensive 3'-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site. Cell. 1991 Mar 22;64(6):1155–1161. doi: 10.1016/0092-8674(91)90270-9. [DOI] [PubMed] [Google Scholar]
  39. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  40. Villemure J. F., Belmaaza A., Chartrand P. The processing of DNA ends at double-strand breaks during homologous recombination: different roles for the two ends. Mol Gen Genet. 1997 Nov;256(5):533–538. doi: 10.1007/s004380050598. [DOI] [PubMed] [Google Scholar]
  41. Zhou Z. H., Akgūn E., Jasin M. Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8326–8333. doi: 10.1073/pnas.151008498. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES