Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Restraining the V(D)J recombinase

Nature Reviews Immunology volume 3, pages 656–666 (2003)Cite this article

Key Points

  • V(D)J recombination allows the vertebrate immune system to generate a diverse array of antigen receptors. Because this process introduces double-strand DNA breaks millions of times each day, it is potentially dangerous.

  • The first step in V(D)J recombination is site recognition and cleavage. The V(D)J recombinase creates a synaptic complex with two recombination signal sequences (RSSs), nicks the DNA between the RSS and the coding flank, and converts the nick to a double-stand break by forming a hairpin at the coding end.

  • The broken DNA ends are then ligated to form a coding joint (the new antigen-receptor gene) and a signal joint (which has no known immunological function).

  • There are three models for recombinase-mediated chromosome translocations: substrate-selection error, end donation and transposition.

  • Factors that help to prevent substrate-selection errors include: the V(D)J recombinase normally requires a pair of RSSs to carry out cleavage (coupled cleavage); chromatin accessibility to the V(D)J recombinase is carefully regulated; and the recombinase has a preference for intralocus recombination.

  • Defences against end donation include: classical non-homologous end joining (NHEJ) minimizes the potential for error (compared with the error-prone alternative NHEJ pathway); and the recombination-activating gene (RAG) post-cleavage complex seems to work closely with classical NHEJ.

  • Defences against transposition include: non-standard products capitalize on the preference of RAG proteins to transpose into hairpin structures; and full-length RAG2 inhibits target capture in the presence of coding ends, and GTP also inhibits target capture.

Abstract

Chromosome breakage — a dangerous event that has triggered the evolution of several double-strand break repair pathways — has been co-opted by the immune system as an integral part of B- and T-cell development. This is a daring strategy, as improper repair can be deadly for the cell, if not for the whole organism. Even more daring, however, is the choice of a promiscuous transposase as the nuclease responsible for chromosome breakage, as the possibility of transposition brings an entirely new set of risks. What mechanisms constrain the dangerous potential of the recombinase and preserve genomic integrity during immune-system development?

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The basic steps of V(D)J recombination.
Figure 2: Non-homologous end joining (NHEJ).
Figure 3: Substrate-selection errors.
Figure 4: End donation.
Figure 5: RAG-mediated transesterification reactions.
Figure 6: Alternative products can be formed by transposition.

Similar content being viewed by others

References

  1. Shaffer, A. L., Rosenwald, A. & Staudt, L. M. Lymphoid malignancies: the dark side of B-cell differentiation. Nature Rev. Immunol. 2, 920–932 (2002).

    Article  CAS  Google Scholar 

  2. Tycko, B. & Sklar, J. Chromosomal translocations in lymphoid neoplasia: a reappraisal of the recombinase model. Cancer Cells 2, 1–8 (1990).

    CAS  PubMed  Google Scholar 

  3. Vanasse, G. J., Concannon, P. & Willerford, D. M. Regulated genomic instability and neoplasia in the lymphoid lineage. Blood 94, 3997–4010 (1999).

    CAS  PubMed  Google Scholar 

  4. Roth, D. B. & Roth, S. Y. Unequal access: regulating V(D)J recombination through chromatin remodeling. Cell 103, 699–702 (2000).

    Article  CAS  PubMed  Google Scholar 

  5. Bassing, C. H., Swat, W. & Alt, F. W. The mechanism and regulation of chromosomal V(D)J recombination. Cell 109, S45–S55 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Lewis, S. M. The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol. 56, 27–150 (1994).

    Article  CAS  PubMed  Google Scholar 

  7. Hesse, J. E., Lieber, M. R., Mizuuchi, K. & Gellert, M. V(D)J recombination: a functional definition of the joining signals. Genes Dev. 3, 1053–1061 (1989).

    Article  CAS  PubMed  Google Scholar 

  8. Oettinger, M. A., Schatz, D. G., Gorka, C. & Baltimore, D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248, 1517–1523 (1990).

    Article  CAS  PubMed  Google Scholar 

  9. van Gent, D. C., Hiom, K., Paull, T. T. & Gellert, M. Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J. 16, 2665–2670 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Silver, D. P., Spanopoulou, E., Mulligan, R. C. & Baltimore, D. Dispensable sequence motifs in the RAG-1 and RAG-2 genes for plasmid V(D)J recombination. Proc. Natl Acad. Sci. USA 90, 6100–6104 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sadofsky, M. J., Hesse, J. E. & Gellert, M. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res. 22, 1805–1809 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Sadofsky, M. J., Hesse, J. E., McBlane, J. F. & Gellert, M. Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 22, 550 (1994).

    Article  CAS  PubMed  Google Scholar 

  13. Cuomo, C. A. & Oettinger, M. A. Analysis of regions of RAG-2 important for V(D)J recombination. Nucleic Acids Res. 22, 1810–1814 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kirch, S. A., Sudarsanam, P. & Oettinger, M. A. Regions of RAG1 protein critical for V(D)J recombination. Eur. J. Immunol. 26, 886–891 (1996).

    Article  CAS  PubMed  Google Scholar 

  15. Roth, D. B., Menetski, J. P., Nakajima, P. B., Bosma, M. J. & Gellert, M. V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes. Cell 70, 983–991 (1992).

    Article  CAS  PubMed  Google Scholar 

  16. Roth, D. B., Zhu, C. & Gellert, M. Characterization of broken DNA molecules associated with V(D)J recombination. Proc. Natl Acad. Sci. USA 90, 10788–10792 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Schlissel, M., Constantinescu, A., Morrow, T., Baxter, M. & Peng, A. Double-strand signal sequence breaks in V(D)J recombination are blunt, 5′-phosphorylated, RAG-dependent, and cell cycle regulated. Genes Dev. 7, 2520–2532 (1993).

    Article  CAS  PubMed  Google Scholar 

  18. McBlane, J. F. et al. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83, 387–395 (1995).

    Article  CAS  PubMed  Google Scholar 

  19. Sadofsky, M. J. The RAG proteins in V(D)J recombination: more than just a nuclease. Nucleic Acids Res. 29, 1399–1409 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71, 101–132 (2002).

    Article  CAS  PubMed  Google Scholar 

  21. van Gent, D. C., Mizuuchi, K. & Gellert, M. Similarities between initiation of V(D)J recombination and retroviral integration. Science 271, 1592–1594 (1996).

    Article  CAS  PubMed  Google Scholar 

  22. Roth, D. B. & Craig, N. L. VDJ recombination: a transposase goes to work. Cell 94, 411–414 (1998).

    Article  CAS  PubMed  Google Scholar 

  23. Kennedy, A. K., Guhathakurta, A., Kleckner, N. & Haniford, D. B. Tn10 transposition via a DNA hairpin intermediate. Cell 95, 125–134 (1998).

    Article  CAS  PubMed  Google Scholar 

  24. Kennedy, A. K., Haniford, D. B. & Mizuuchi, K. Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity. Cell 101, 295–305 (2000).

    Article  CAS  PubMed  Google Scholar 

  25. Davies, D. R., Goryshin, I. Y., Reznikoff, W. S. & Rayment, I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289, 77–85 (2000).

    Article  CAS  PubMed  Google Scholar 

  26. Coen, E., Robbins, T. P., Almeida, J., Hudson, A. & Carpenter, R. in Mobile DNA (eds Berg, D. E. & Howe, M. M.) 413–436 (ASM Press, Washington DC, 1989).

    Google Scholar 

  27. Weil, C. F. & Kunze, R. Transposition of maize Ac/Ds transposable elements in the yeast Saccharomyces cerevisiae. Nature Genet. 26, 187–190 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Kunze, R. & Weil, C. F. in Mobile DNA II (ed. Craig, N. L.) 565–610 (ASM Press, Washington DC, 2002).

    Book  Google Scholar 

  29. Ramsden, D. A., McBlane, J. F., van Gent, D. C. & Gellert, M. Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. EMBO J. 15, 3197–3206 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Eastman, Q. M. & Schatz, D. G. Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage. Nucleic Acids Res. 25, 4370–4378 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. van Gent, D. C., Ramsden, D. A. & Gellert, M. The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 85, 107–113 (1996).

    Article  CAS  PubMed  Google Scholar 

  32. Yu, K. & Lieber, M. R. The nicking step in V(D)J recombination is independent of synapsis: implications for the immune repertoire. Mol. Cell. Biol. 20, 7914–7921 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Steen, S. B., Gomelsky, L. & Roth, D. B. The 12/23 rule is enforced at the cleavage step of V(D)J recombination in vivo. Genes Cells 1, 543–553 (1996).

    Article  CAS  PubMed  Google Scholar 

  34. Eastman, Q. M., Leu, T. M. J. & Schatz, D. G. Initiation of V(D)J recombination in vitro: obeying the 12/23 rule. Nature 380, 85–88 (1996).

    Article  CAS  PubMed  Google Scholar 

  35. Bassing, C. H. et al. Recombination signal sequences restrict chromosomal V(D)J recombination beyond the 12/23 rule. Nature 405, 583–586 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Tillman, R. E. et al. Cutting edge: targeting of Vβ to Dβ rearrangement by RSSs can be mediated by the V(D)J recombinase in the absence of additional lymphoid-specific factors. J. Immunol. 170, 5–9 (2003).

    Article  CAS  PubMed  Google Scholar 

  37. Jung, D. et al. Extrachromosomal recombination substrates recapitulate beyond 12/23 restricted VDJ recombination in nonlymphoid cells. Immunity 18, 65–74 (2003).

    Article  CAS  PubMed  Google Scholar 

  38. Lewis, S. M., Hesse, J. E., Mizuuchi, K. & Gellert, M. Novel strand exchanges in V(D)J recombination. Cell 55, 1099–1107 (1988).

    Article  CAS  PubMed  Google Scholar 

  39. Morzycka-Wroblewska, E., Lee, F. & Desiderio, S. Unusual immunoglobulin gene rearrangement leads to replacement of recombination signal sequences. Science 242, 261–263 (1988).

    Article  CAS  PubMed  Google Scholar 

  40. Carroll, A. M., Slack, J. K. & Mu, X. V(D)J recombination generates a high frequency of nonstandard TCRδ-associated rearrangements in thymocytes. J. Immunol. 150, 2222–2230 (1993).

    CAS  PubMed  Google Scholar 

  41. Bogue, M. A., Wang, C., Zhu, C. & Roth, D. B. V(D)J recombination in Ku86-deficient mice: distinct effects on coding, signal and hybrid joint formation. Immunity 7, 37–47 (1997).

    Article  CAS  PubMed  Google Scholar 

  42. Sollbach, A. E. & Wu, G. E. Inversions produced during V(D)J rearrangement at IgH, the immunoglobulin heavy-chain locus. Mol. Cell. Biol. 15, 671–681 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. VanDyk, L. F., Wise, T. W., Moore, B. B. & Meek, K. Immunoglobulin DH recombination signal sequence targeting. J. Immunol. 157, 4005–4015 (1996).

    CAS  PubMed  Google Scholar 

  44. Grawunder, U. & Harfst, E. How to make ends meet in V(D)J recombination. Curr. Opin. Immunol. 13, 186–194 (2001).

    Article  CAS  PubMed  Google Scholar 

  45. Dai, Y. et al. Nonhomologous end joining and V(D)J recombination require an additional factor. Proc. Natl Acad. Sci. USA 100, 2462–2467 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Walker, J. R., Corpina, R. A. & Goldberg, J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412, 607–614 (2001).

    Article  CAS  PubMed  Google Scholar 

  47. Mahajan, K. N. et al. Association of terminal deoxynucleotidyl transferase with Ku. Proc. Natl Acad. Sci. USA 96, 13926–13931 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Purugganan, M. M., Shah, S., Kearney, J. F. & Roth, D. B. Ku80 is required for addition of N nucleotides to V(D)J recombination junctions by terminal deoxynucleotidyl transferase. Nucleic Acids Res. 29, 1638–1646 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zhu, C., Bogue, M. A., Lim, D. -S., Hasty, P. & Roth, D. B. Ku86-deficient mice exhibit severe combined immunodeficiency and defective processing of V(D)J recombination intermediates. Cell 86, 379–389 (1996).

    Article  CAS  PubMed  Google Scholar 

  50. Leber, R., Wise, T. W., Mizuta, R. & Meek, K. The XRCC4 gene product is a target for and interacts with the DNA-dependent protein kinase. J. Biol. Chem. 273, 1794–1801 (1998).

    Article  CAS  PubMed  Google Scholar 

  51. Ma, Y., Pannicke, U., Schwarz, K. & Lieber, M. R. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108, 781–794 (2002). This paper describes biochemical evidence that Artemis opens hairpin coding ends and provides a mechanistic link between Artemis, hairpin opening and DNA-dependent protein kinase (DNA-PK).

    Article  CAS  PubMed  Google Scholar 

  52. Mahajan, K. N., Nick McElhinny, S. A., Mitchell, B. S. & Ramsden, D. A. Association of DNA polymerase μ (pol μ) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair. Mol. Cell. Biol. 22, 5194–5202 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Critchlow, S. E., Bowater, R. P. & Jackson, S. P. Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV. Curr. Biol. 7, 588–598 (1997).

    Article  CAS  PubMed  Google Scholar 

  54. Grawunder, U. et al. Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 388, 492–495 (1997).

    Article  CAS  PubMed  Google Scholar 

  55. Modesti, M., Hesse, J. E. & Gellert, M. DNA binding of XRCC4 protein is associated with V(D)J recombination but not with stimulation of DNA ligase IV activity. EMBO J. 18, 2008–2018 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Qiu, J. X., Kale, S. B., Yarnell Schultz, H. & Roth, D. B. Separation-of-function mutants reveal critical roles for RAG2 in both the cleavage and joining steps of V(D)J recombination. Mol. Cell 7, 77–87 (2001).

    Article  CAS  PubMed  Google Scholar 

  57. Yarnall Schultz, H., Landree, M. A., Qiu, J. X., Kale, S. B. & Roth, D. B. Joining-deficient RAG1 mutants block V(D)J recombination in vivo and hairpin opening in vitro. Mol. Cell 7, 65–75 (2001). Separation-of-function mutants in recombination-activating gene 1 ( RAG1 ) in this and reference 58 provided the first evidence that the RAG post-cleavage complex is crucial for joining, functioning as a scaffold for both coding and signal ends in living cells.

    Article  Google Scholar 

  58. Huye, L. E., Purugganan, M. M., Jiang, M. M. & Roth, D. B. Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase. Mol. Cell. Biol. 22, 3460–3473 (2002). Cells that express joining-deficient RAG1 mutants produce joints with the same kinds of abnormalities that are seen in non-homologous end joining (NHEJ)-deficient mutants, providing evidence that the RAG proteins actively collaborate with the classical NHEJ pathway.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Rooney, S. et al. Leaky scid phenotype associated with defective V(D)J coding end processing in Artemis-deficient mice. Mol. Cell 10, 1379–1390 (2002). An Artemis-knockout mouse confirms that Artemis does indeed have an important role in opening hairpin-coding ends, but the leaky phenotype of these mice hints that alternative pathways might also carry out this function. This paper also shows that Artemis deficiency leads to genomic instability in fibroblasts.

    Article  CAS  PubMed  Google Scholar 

  60. Besmer, E. et al. Hairpin coding end opening is mediated by RAG1 and RAG2 proteins. Mol. Cell 2, 817–828 (1998).

    Article  CAS  PubMed  Google Scholar 

  61. Shockett, P. E. & Schatz, D. G. DNA hairpin opening mediated by the RAG1 and RAG2 proteins. Mol. Cell. Biol. 19, 4159–4166 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Paull, T. T. & Gellert, M. The 3′ to 5′ exonuclease activity of Mre11 facilitates repair of DNA double-strand breaks. Mol. Cell 1, 969–979 (1998).

    Article  CAS  PubMed  Google Scholar 

  63. Mansilla-Soto, J. & Cortes, P. VDJ recombination: Artemis and its in vivo role in hairpin opening. J. Exp. Med. 197, 543–547 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Yurchenko, V., Xue, Z. & Sadofsky, M. The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev. 17, 581–585 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Vanasse, G. J. et al. Genetic pathway to recurrent chromosome translocations in murine lymphoma involves V(D)J recombinase. J. Clin. Invest. 103, 1669–1675 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Kuppers, R. & Dalla-Favera, R. Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene 20, 5580–5594 (2001).

    Article  CAS  PubMed  Google Scholar 

  67. Kirsch, I. R., Morton, C. C., Nakahara, K. & Leder, P. Human immunoglobulin heavy chain genes map to a region of translocations in malignant B lymphocytes. Science 216, 301–303 (1982).

    Article  CAS  PubMed  Google Scholar 

  68. Dalla-Favera, R. et al. Human c-myc oncogene is located on the region of chromosome 8 that is translocated in Burkitt lymphoma cells. Proc. Natl Acad. Sci. USA 79, 7824–7827 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Tycko, B., Palmer, J. D. & Sklar, J. T cell receptor gene trans-rearrangements: chimeric γδ genes in normal lymphoid tissues. Science 245, 1242–1246 (1989).

    Article  CAS  PubMed  Google Scholar 

  70. Tycko, B., Coyle, H. & Sklar, J. Chimeric γδ signal joints: implications for the mechanism and regulation of T cell receptor gene rearrangement. J. Immunol. 147, 705–713 (1991).

    CAS  PubMed  Google Scholar 

  71. Bailey, S. N. & Rosenberg, N. Assessing the pathogenic potential of the V(D)J recombinase by interlocus immunoglobulin light-chain gene rearrangement. Mol. Cell. Biol. 17, 887–894 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Kobayashi, Y., Tycko, B., Soreng, A. L. & Sklar, J. Transrearrangements between antigen receptor genes in normal human lymphoid tissues and in ataxia telangiectasia. J. Immunol. 147, 3201–3209 (1991).

    CAS  PubMed  Google Scholar 

  73. Lipkowitz, S., Stern, M. H. & Kirsch, I. R. Hybrid T cell receptor genes formed by interlocus recombination in normal and ataxia-telangiectasia lymphocytes. J. Exp. Med. 172, 409–418 (1990).

    Article  CAS  PubMed  Google Scholar 

  74. Kirsch, I. R. & Lipkowitz, S. A measure of genomic instability and its relevance to lymphomagenesis. Cancer Res. 52, 5545s–5546s (1992).

    CAS  PubMed  Google Scholar 

  75. Steen, S. B., Gomelsky, L., Speidel, S. L. & Roth, D. B. Initiation of V(D)J recombination in vivo: role of recombination signal sequences in formation of single and paired double-strand breaks. EMBO J. 16, 2656–2664 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Bakhshi, A. et al. Mechanism of the t(14;18) chromosomal translocation: structural analysis of both derivative 14 and 18 reciprocal partners. Proc. Natl Acad. Sci. USA 84, 2396–2400 (1987). The initial description of the end-donation model for RAG-mediated chromosome translocations. Evidence that this is a common mechanism for lymphomagenesis is also provided in references 77 and 78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Welzel, N. et al. Templated nucleotide addition and immunoglobulin JH-gene utilization in t(11;14) junctions: implications for the mechanism of translocation and the origin of mantle cell lymphoma. Cancer Res. 61, 1629–1636 (2001).

    CAS  PubMed  Google Scholar 

  78. Jager, U. et al. Follicular lymphomas' BCL-2/IgH junctions contain templated nucleotide insertions: novel insights into the mechanism of t(14;18) translocation. Blood 95, 3520–3529 (2000).

    CAS  PubMed  Google Scholar 

  79. Han, J. -O., Steen, S. B. & Roth, D. B. Ku86 is not required for protection of signal ends or for formation of nonstandard V(D)J recombination products. Mol. Cell. Biol. 17, 2226–2234 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Han, J. -O., Erskine, L. A., Purugganan, M. M., Stamato, T. D. & Roth, D. B. V(D)J recombination intermediates and non-standard products in XRCC4-deficient cells. Nucleic Acids Res. 26, 3769–3775 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Melek, M., Gellert, M. & van Gent, D. C. Rejoining of DNA by the RAG1 and RAG2 proteins. Science 280, 301–303 (1998).

    Article  CAS  PubMed  Google Scholar 

  82. Agrawal, A., Eastman, Q. M. & Schatz, D. G. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394, 744–751 (1998).

    Article  CAS  PubMed  Google Scholar 

  83. Hiom, K., Melek, M. & Gellert, M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94, 463–470 (1998). These authors show that the RAG proteins are capable of transposition in the test tube, and they propose several models for transposition-mediated genome rearrangements.

    Article  CAS  PubMed  Google Scholar 

  84. Thompson, C. B. New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3, 531–539 (1995).

    Article  CAS  PubMed  Google Scholar 

  85. Messier, T. L., O'Neill, J. P., Hou, S. M., Nicklas, J. A. & Finette, B. A. In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J. 22, 1381–1388 (2003). The first reported evidence for RAG-mediated transposition in vivo.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Lee, G. S., Neiditch, M. B., Sinden, R. R. & Roth, D. B. Targeted transposition by the V(D)J recombinase. Mol. Cell. Biol. 22, 2068–2077 (2002). This work shows that RAG-mediated transposition is strongly targeted to hairpin ends and provides evidence that nonstandard junctions (hybrid and open-and-shut joints) can form by transposition, indicating that the formation of these products in vivo might function as a safety mechanism to prevent more dangerous transposition events.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Roth, D. B., Nakajima, P. B., Menetski, J. P., Bosma, M. J. & Gellert, M. V(D)J recombination in mouse thymocytes: double-strand breaks near T cell receptor δ rearrangement signals. Cell 69, 41–53 (1992).

    Article  CAS  PubMed  Google Scholar 

  88. Tillman, R. E. et al. Restrictions limiting the generation of DNA double strand breaks during chromosomal V(D)J recombination. J. Exp. Med. 195, 309–316 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158–162 (2002).

    Article  CAS  PubMed  Google Scholar 

  90. Barlow, C. et al. Atm-deficient mice: a paradigm of ataxia telangiectasia. Cell 86, 159–171 (1996).

    Article  CAS  PubMed  Google Scholar 

  91. Taylor, A. M., Metcalfe, J. A., Thick, J. & Mak, Y. F. Leukemia and lymphoma in ataxia telangiectasia. Blood 87, 423–438 (1996).

    CAS  PubMed  Google Scholar 

  92. Xu, Y. et al. Targeted disruption of ATM leads to growth retardation, chromosomal fragmentation during meiosis, immune defects, and thymic lymphoma. Genes Dev. 10, 2411–2422 (1996).

    Article  CAS  PubMed  Google Scholar 

  93. Liyanage, M. et al. Abnormal rearrangement within the αδ T-cell receptor locus in lymphomas from Atm-deficient mice. Blood 96, 1940–1946 (2000).

    CAS  PubMed  Google Scholar 

  94. Lista, F., Bertness, V., Guidos, C. J., Danska, J. S. & Kirsch, I. R. The absolute number of trans-rearrangements between the TCR γ and TCR β loci is predictive of lymphoma risk: a severe combined immune deficiency (SCID) murine model. Cancer Res. 57, 4408–4413 (1997).

    CAS  PubMed  Google Scholar 

  95. Perkins, E. J. et al. Sensing of intermediates in V(D)J recombination by ATM. Genes Dev. 16, 159–164 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Han, J. -O., Steen, S. B. & Roth, D. B. Intermolecular V(D)J recombination is prohibited specifically at the joining step. Mol. Cell 3, 331–338 (1999).

    Article  CAS  PubMed  Google Scholar 

  97. Tevelev, A. & Schatz, D. G. Intermolecular V(D)J recombination. J. Biol. Chem. 275, 8341–8348 (2000).

    Article  CAS  PubMed  Google Scholar 

  98. Hempel, W. M. et al. Enhancer control of V(D)J recombination at the TCR β locus: differential effects on DNA cleavage and joining. Genes Dev. 12, 2305–2317 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. 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 17, 5497–5508 (1998).

    Article  CAS  Google Scholar 

  100. Paques, F. & Haber, J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63, 349–404 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Cox, M. M. et al. The importance of repairing stalled replication forks. Nature 404, 37–41 (2000).

    Article  CAS  PubMed  Google Scholar 

  102. Ferguson, D. O. & Alt, F. W. DNA double strand break repair and chromosomal translocation: lessons from animal models. Oncogene 20, 5572–5579 (2001).

    Article  CAS  PubMed  Google Scholar 

  103. Zhu, C. et al. Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations. Cell 109, 811–821 (2002). Complex chromosomal rearrangements and gene amplification occur in mice that are doubly deficient for classic NHEJ and p53, implicating alternative, microhomology-mediated joining pathways.

    Article  CAS  PubMed  Google Scholar 

  104. Jackson, S. P. Sensing and repairing DNA double-strand breaks. Carcinogenesis 23, 687–696 (2002).

    Article  CAS  PubMed  Google Scholar 

  105. Ferguson, D. O. et al. The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc. Natl Acad. Sci. USA 97, 6630–6633 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Jhappan, C., Morse, H. C., Fleischmann, R. D., Gottesman, M. M. & Merlino, G. DNA-PKcs: a T-cell tumour suppressor encoded at the mouse scid locus. Nature Genet. 17, 483–486 (1997).

    Article  CAS  PubMed  Google Scholar 

  107. Custer, R. P., Bosma, G. C. & Bosma, M. J. Severe combined immunodeficiency in the mouse: pathology, reconstitution, neoplasms. Am. J. Pathol. 120, 464–477 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Gu, Y. et al. Growth retardation and leaky SCID phenotype of Ku70-deficient mice. Immunity 7, 653–665 (1997).

    Article  CAS  PubMed  Google Scholar 

  109. Li, G. C. et al. Ku70: a candidate tumor suppressor gene for murine T cell lymphoma. Mol. Cell 2, 1–8 (1998).

    Article  CAS  PubMed  Google Scholar 

  110. Difilippantonio, M. J. et al. DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation. Nature 404, 510–514 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Gao, Y. et al. Interplay of p53 and DNA-repair protein XRCC4 in tumorigenesis, genomic stability and development. Nature 404, 897–900 (2000).

    Article  CAS  PubMed  Google Scholar 

  112. Moshous, D. et al. Partial T and B lymphocyte immunodeficiency and predisposition to lymphoma in patients with hypomorphic mutations in Artemis. J. Clin. Invest. 111, 381–387 (2003). Artemis mutations predispose to lymphoma in humans, indicating that Artemis functions as a genome guardian.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Gladdy, R. A. et al. The RAG-1/2 endonuclease causes genomic instability and controls CNS complications of lymphoblastic leukemia in p53/Prkdc-deficient mice. Cancer Cell 3, 37–50 (2003).

    Article  CAS  PubMed  Google Scholar 

  114. Sharpless, N. E. et al. Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions. Mol. Cell 8, 1187–1196 (2001).

    Article  CAS  PubMed  Google Scholar 

  115. Williams, C. J. et al. Irradiation promotes V(D)J joining and RAG-dependent neoplastic transformation in SCID T-cell precursors. Mol. Cell. Biol. 21, 400–413 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Danska, J. S. et al. Rescue of T cell-specific V(D)J recombination in SCID mice by DNA damaging agents. Science 266, 450–455 (1994).

    Article  CAS  PubMed  Google Scholar 

  117. Murphy, W. J. et al. Induction of T cell differentiation and lymphomagenesis in the thymus of mice with severe combined immunodeficiency (SCID). J. Immunol. 153, 1004–1014 (1994).

    CAS  PubMed  Google Scholar 

  118. Wilson, J. H., Berget, P. B. & Pipas, J. M. Somatic cells efficiently join unrelated DNA segments end-to-end. Mol. Cell. Biol. 2, 1258–1269 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Roth, D. B., Porter, T. N. & Wilson, J. H. Mechanisms of nonhomologous recombination in mammalian cells. Mol. Cell. Biol. 5, 2599–2607 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Roth, D. B. & Wilson, J. H. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol. Cell. Biol. 6, 4295–4304 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Kabotyanski, E. B., Gomelsky, L., Han, J. -O., Stamato, T. D. & Roth, D. B. Double-strand break repair in Ku86- and XRCC4-deficient cells. Nucleic Acids Res. 26, 5333–5342 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Baumann, P. & West, S. C. DNA end-joining catalyzed by human cell-free extracts. Proc. Natl Acad. Sci. USA 95, 14066–14070 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Roth, D. B. Amplifying mechanisms of lymphomagenesis. Mol. Cell 10, 1–2 (2002).

    Article  CAS  PubMed  Google Scholar 

  124. Verkaik, N. S. et al. Different types of V(D)J recombination and end-joining defects in DNA double-strand break repair mutant mammalian cells. Eur. J. Immunol. 32, 701–709 (2002).

    Article  CAS  PubMed  Google Scholar 

  125. Agrawal, A. & Schatz, D. G. RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89, 43–53 (1997).

    Article  CAS  PubMed  Google Scholar 

  126. Hiom, K. & Gellert, M. Assembly of a 12/23 paired signal complex: a critical control point in V(D)J recombination. Mol. Cell 1, 1011–1019 (1998).

    Article  CAS  PubMed  Google Scholar 

  127. Jones, J. M. & Gellert, M. Intermediates in V(D)J recombination: a stable RAG1/2 complex sequesters cleaved RSS ends. Proc. Natl Acad. Sci. USA 98, 12926–12931 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Ramsden, D. A., Paull, T. T. & Gellert, M. Cell-free V(D)J recombination. Nature 388, 488–491 (1997).

    Article  CAS  PubMed  Google Scholar 

  129. Brandt, V. L. & Roth, D. B. A recombinase diversified: new functions of the RAG proteins. Curr. Opin. Immunol. 14, 224–229 (2002).

    Article  CAS  PubMed  Google Scholar 

  130. Tsai, C. L., Drejer, A. H. & Schatz, D. G. Evidence of a critical architectural function for the RAG proteins in end processing, protection, and joining in V(D)J recombination. Genes Dev. 16, 1934–1949 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Neiditch, M. B., Lee, G. S., Huye, L. E., Brandt, V. L. & Roth, D. B. The V(D)J recombinase efficiently cleaves and transposes signal joints. Mol. Cell 9, 871–878 (2002).

    Article  CAS  PubMed  Google Scholar 

  132. Zhu, C. & Roth, D. B. Characterization of coding ends in thymocytes of scid mice: implications for the mechanism of V(D)J recombination. Immunity 2, 101–112 (1995).

    Article  CAS  PubMed  Google Scholar 

  133. Marculescu, R. et al. Distinct t(7;9)(q34;q32) breakpoints in healthy individuals and individuals with T-ALL. Nature Genet. 33, 342–344 (2003). This work implicates signal joints in oncogenic chromosome translocations; see also reference 131.

    Article  CAS  PubMed  Google Scholar 

  134. Melek, M. & Gellert, M. RAG1/2-mediated resolution of transposition intermediates: two pathways and possible consequences. Cell 101, 625–633 (2000).

    Article  CAS  PubMed  Google Scholar 

  135. Sekiguchi, J. A., Whitlow, S. & Alt, F. W. Increased accumulation of hybrid V(D)J joins in cells expressing truncated versus full-length RAGs. Mol. Cell 8, 1383–1390 (2001).

    Article  CAS  PubMed  Google Scholar 

  136. Elkin, S. K., Matthews, A. G. & Oettinger, M. A. The C-terminal portion of RAG2 protects against transposition in vitro. EMBO J. 22, 1931–1938 (2003). This paper shows that the carboxyl terminus of RAG2 helps to prevent transposition in vitro in the presence of coding ends.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Tsai, C. L. & Schatz, D. G. Regulation of RAG1/RAG2-mediated transposition by GTP and the C-terminal region of RAG2. EMBO J. 22, 1922–1930 (2003). More evidence that the carboxyl terminus of RAG2 downregulates transposition in vitro ; furthermore, the authors find that GTP modulates transposition activity in vitro.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Livak, F. & Schatz, D. G. T-cell receptor α locus V(D)J recombination by-products are abundant in thymocytes and mature T cells. Mol. Cell. Biol. 16, 609–618 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

I am grateful to S. Lewis, J. Petrini, M. Schlissel, G. Wu, K. Meek, N. Craig, G. Lee and V. Brandt for helpful discussions. I also thank G. Lee for providing figure 2. Work in my laboratory is supported by grants from the National Institutes of Health and by the Irene Diamond Foundation.

Author information

Authors and Affiliations

  1. Department of Pathology, Program in Molecular Pathogenesis, Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, 10016, USA

    David B. Roth

Authors
  1. David B. Roth
    View author publications

    You can also search for this author in PubMed Google Scholar

Related links

Related links

DATABASES

LocusLink

Artemis

ATM

DNA ligase IV

DNA-PKcs

DNA polymerase μ

HMG1

HMG2

HPRT

Ku70

Ku86

Mre11

p53

RAG1

RAG2

XRCC4

Glossary

TRANSPOSASE

A protein that carries out transposition — that is, moves a segment of DNA from one position in the genome to another position (or to a different genome).

NON-HOMOLOGOUS END JOINING

(NHEJ). One of the two main double-strand break repair pathways, the other being homologous recombination. An 'alternative NHEJ pathway' that does not depend on the six known NHEJ factors (Ku70, Ku86, DNA-PKcs, XRCC4, Artemis and DNA ligase IV) has been described, but it is not well understood.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Roth, D. Restraining the V(D)J recombinase. Nat Rev Immunol 3, 656–666 (2003). https://doi.org/10.1038/nri1152

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nri1152

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing