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:

The mechanisms of immune diversification and their disorders

Nature Reviews Immunology volume 3, pages 962–972 (2003)Cite this article

Key Points

  • V(D)J recombination, class-switch recombination (CSR) and somatic hypermutation (SHM) are accompanied by DNA damage/modification, and defects in these processes cause various immune deficiencies.

  • Mutations of the V(D)J recombination/DNA-repair factor Artemis cause severe combined immunodeficiency with an absence of T and B cells (T-B-SCID) with increased radiosensitivity.

  • Artemis belongs to the metallo-β-lactamase family and is involved in opening recombinase-activating gene 1 (RAG1)/RAG2-generated hairpins during V(D)J recombination.

  • Hypomorphic mutations of Artemis are accompanied by the development of B-cell lymphomas; Artemis is a genome 'caretaker'.

  • CSR and SHM require CD40 activation. Hyper-IgM syndromes (HIGMs) are characterized by a defect of CSR with or without a defect in SHM.

  • Activation-induced cytidine deaminase (AID) is a cytidine deaminase that is induced by CD40 activation and that is required for CSR and SHM.

  • AID — a possible DNA-editing enzyme — is involved in CSR-induced DNA breaks.

Abstract

Three molecular mechanisms contribute to the diversity of the immune repertoire of B and T cells: V(D)J recombination generates the primary repertoire in both cases, whereas class-switch recombination (CSR) and somatic hypermutation (SHM) improve the quality of the B-cell response after antigen triggering. These three mechanisms involve marked DNA damage and modification, which require a fully competent cellular DNA-repair machinery. Defects in V(D)J recombination, CSR or SHM reactions lead to immune deficiencies, the study of which has allowed the identification of genes that are central to these processes. The inability to properly manage DNA damage/modification during V(D)J recombination, can also promote the development of cancer, as shown by the emergence of B-cell lymphomas in patients with a partial Artemis defect.

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: Organization of the human immunoglobulin IgH locus and its somatic modifications to generate a primary and secondary B-cell repertoire.
Figure 2: Blockade of lymphoid development in humans with severe combined immunodeficiency (SCID).
Figure 3: V(D)J recombination.
Figure 4: Artemis.
Figure 5: Schematic representation of a germinal centre (GC) in which CSR and SHM of GC founder B cells (CD38+IgM+IgD+) occur in cooperation with activated CD4+ T cells.
Figure 6: CSR and SHM share two common mechanisms: transcription of targeted DNA and DNA cleavage.
Figure 7: NHEJ factors are genome caretakers.

Similar content being viewed by others

References

  1. Tonegawa, S. Somatic generation of antibody diversity. Nature 302, 575–581 (1983).

    Article  CAS  PubMed  Google Scholar 

  2. 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 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  5. Honjo, T., Kinoshita, K. & Muramatsu, M. Molecular mechansism of class switch recombination: linkage with somatic hypermutation. Annu. Rev. Immunol. 20, 165–196 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Fischer, A. Primary immunodeficiency diseases: an experimental model for molecular medicine. Lancet 357, 1863–1869 (2001).

    CAS  PubMed  Google Scholar 

  7. Haber, J. E. Partners and pathways repairing a double-strand break. Trends Genet. 16, 259–264 (2000).

    CAS  PubMed  Google Scholar 

  8. Mombaerts, P. et al. RAG-1 deficient mice have no mature B and T lymphocytes. Cell 68, 869–877 (1992).

    CAS  PubMed  Google Scholar 

  9. Shinkai, Y. et al. RAG-2 deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68, 855–867 (1992).

    CAS  PubMed  Google Scholar 

  10. Schwarz, K. et al. RAG mutations in human B cell-negative SCID. Science 274, 97–99 (1996).

    CAS  PubMed  Google Scholar 

  11. de Villartay, J. P. V(D)J recombination and DNA repair: lessons from human immune deficiencies and other animal models. Curr. Opin. Allergy Clin. Immunol. 2, 473–479 (2002).

    PubMed  Google Scholar 

  12. Callebaut, I. & Mornon, J. P. The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis. Cell. Mol. Life Sci. 54, 880–891 (1998).

    CAS  PubMed  Google Scholar 

  13. Corneo, B. et al. 3D clustering of human RAG2 gene mutations in severe combined immune deficiency (SCID). J. Biol. Chem. 275, 12672–12675 (2000).

    CAS  PubMed  Google Scholar 

  14. Fugmann, S. D., Lee, A. I., Shockett, P. E., Villey, I. J. & Schatz, D. G. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 18, 495–527 (2000).

    CAS  PubMed  Google Scholar 

  15. Li, Z., Dordai, D. I., Lee, J. & Desiderio, S. A conserved degradation signal regulates RAG-2 accumulation during cell division and links V(D)J recombination to the cell cycle. Immunity 5, 575–589 (1996).

    PubMed  Google Scholar 

  16. Villa, A. et al. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 97, 81–88 (2001).

    CAS  PubMed  Google Scholar 

  17. Liang, H. E. et al. The 'dispensable' portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development. Immunity 17, 639–651 (2002).

    CAS  PubMed  Google Scholar 

  18. Akamatsu, Y. et al. Deletion of the RAG2 C terminus leads to impaired lymphoid development in mice. Proc. Natl Acad. Sci. USA 100, 1209–1214 (2003). References 17 and 18 describe the development of knock-in mice that express only the core of recombinase-activating gene 2 (Rag2), showing the absolute requirement of full length Rag2 for the proper rearrangement of endogenous immuno-globulin and T-cell receptor (TCR) loci in vivo.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Roman, C. A., Cherry, S. R. & Baltimore, D. Complementation of V(D)J recombination deficiency in RAG-1−/− B cells reveals a requirement for novel elements in the N-terminus of RAG-1. Immunity 7, 13–24 (1997).

    CAS  PubMed  Google Scholar 

  20. Kirch, S. A., Rathbun, G. A. & Oettinger, M. A. Dual role of RAG2 in V(D)J recombination: catalysis and regulation of ordered Ig gene assembly. EMBO J. 17, 4881–4886 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Corneo, B., Benmerah, A. & de Villartay, J. P. A short peptide at the C-terminus is responsible for the nuclear localization of RAG2. Eur. J. Immunol. 32, 2068–2073 (2002).

    CAS  PubMed  Google Scholar 

  22. Ross, A. E., Vuica, M. & Desiderio, S. Overlapping signals for protein degradation and nuclear localization define a role for intrinsic RAG-2 nuclear uptake in dividing cells. Mol. Cell Biol. 23, 5308–5319 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Aasland, R., Gibson, T. J. & Stewart, A. F. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci. 20, 56–59 (1995).

    CAS  PubMed  Google Scholar 

  24. Villa, A., Sobacchi, C. & Vezzoni, P. Recombination activating gene and its defects. Curr. Opin. Allergy Clin. Immunol. 1, 491–495 (2001).

    CAS  PubMed  Google Scholar 

  25. Corneo, B. et al. Identical mutations in RAG1 and RAG2 genes leading to defective V(D)Jrecombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood 97, 2772–2776 (2001).

    CAS  PubMed  Google Scholar 

  26. Cavazzana-Calvo, M. et al. Increased radiosensitivity of granulocyte macrophage colony-forming units and skin fibroblasts in human autosomal recessive severe combined immunodeficiency. J. Clin. Invest. 91, 1214–1218 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Bosma, M. J. & Carroll, A. M. The SCID mouse mutant: definition, characterization, and potential uses. Annu. Rev. Immunol. 9, 323–350 (1991).

    CAS  PubMed  Google Scholar 

  28. Nicolas, N. et al. A human SCID condition with increased sensitivity to ionizing radiations and impaired V(D)J rearrangements defines a new DNA recombination/repair deficiency. J. Exp. Med. 188, 627–634 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Nicolas, N. et al. Lack of detectable defect in DNA double-strand break repair and DNA-dependant protein kinase activity in radiosensitive human severe combined immunodeficiency fibroblasts. Eur. J. Immunol. 26, 1118–1122 (1996).

    CAS  PubMed  Google Scholar 

  30. Li, L. et al. The gene for severe combined immunodeficiency disease in Athabascan-speaking native americans is located on chromosome 10p. Am. J. Hum. Genet. 62, 136–144 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Moshous, D. et al. A new gene involved in DNA double-strand break repair and V(D)J recombination is located on human chromosome 10p. Hum. Mol. Genet. 9, 583–588 (2000).

    CAS  PubMed  Google Scholar 

  32. Moshous, D. et al. Artemis, a novel DNA double-strand break repair/V(D)J recombination protein, is mutated in human severe combined immune deficiency. Cell 105, 177–186 (2001). This reference describes the cloning of the human Artemis gene from the analysis of patients with radiosensitive-severe combined immunodeficiency (RS-SCID).

    CAS  PubMed  Google Scholar 

  33. Li, L. et al. A founder mutation in Artemis, an SNM1-like protein, causes SCID in Athabascan-speaking native Americans. J. Immunol. 168, 6323–6329 (2002).

    CAS  PubMed  Google Scholar 

  34. Noordzij, J. G. et al. Radiosensitive SCID patients with Artemis gene mutations show a complete B-cell differentiation arrest at the pre-B-cell receptor checkpoint in bone marrow. Blood 101, 1446–1452 (2003).

    CAS  PubMed  Google Scholar 

  35. Kobayashi, N. et al. Novel Artemis gene mutations of radiosensitive severe combined immunodeficiency in Japanese families. Hum. Genet. 112, 348–352 (2003).

    CAS  PubMed  Google Scholar 

  36. 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). This paper provides a description of Artemis-knockout mice.

    CAS  PubMed  Google Scholar 

  37. Aravind, L. An evolutionary classification of the metallo-β-lactamase fold. In Silico Biology 1, 69–91 (1999).

    CAS  PubMed  Google Scholar 

  38. Callebaut, I., Moshous, D., Mornon, J. P. & De Villartay, J. P. Metallo-β-lactamase fold within nucleic acids processing enzymes: the β-CASP family. Nucl. Acids Res. 30, 3592–3601 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 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).

    CAS  PubMed  Google Scholar 

  40. 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). The first evidence that Artemis, when complexed to the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), is capable of opening RAG1/RAG2-generated hairpin structures.

    CAS  PubMed  Google Scholar 

  41. 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).

    CAS  PubMed  Google Scholar 

  42. 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).

    CAS  PubMed  Google Scholar 

  43. Yarnell 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).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  46. Paull, T. T. & Gellert, M. Nbs1 potentiates ATP-driven DNA unwinding and endonuclease cleavage by the Mre11/Rad50 complex. Genes Dev. 13, 1276–1288 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Chen, H. T. et al. Response to RAG-mediated V(D)J cleavage by NBS1 and γ-H2AX. Science 290, 1962–1965 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Harfst, E., Cooper, S., Neubauer, S., Distel, L. & Grawunder, U. Normal V(D)J recombination in cells from patients with Nijmegen breakage syndrome. Mol. Immunol. 37, 915–929 (2000).

    CAS  PubMed  Google Scholar 

  49. Barnes, D. E., Stamp, G., Rosewell, I., Denzel, A. & Lindahl, T. Targeted disruption of the gene encoding DNA ligase IV leads to lethality in embryonic mice. Curr. Biol. 8, 1395–1398 (1998).

    CAS  PubMed  Google Scholar 

  50. Gao, Y. et al. A critical role for DNA end-joining proteins in both lymphogenesis and neurogenesis. Cell 95, 891–902 (1998).

    CAS  PubMed  Google Scholar 

  51. Frank, K. M. et al. Late embryonic lethality and impaired V(D)J recombination in mice lacking DNA ligase IV. Nature 396, 173–177 (1998).

    CAS  PubMed  Google Scholar 

  52. O'Driscoll, M. et al. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Mol. Cell 8, 1175–1185 (2001). A description of DNA ligase IV deficiency in humans.

    CAS  PubMed  Google Scholar 

  53. Riballo, E. et al. Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radiosensitivity. J. Biol. Chem. 276, 31124–31132 (2001).

    CAS  PubMed  Google Scholar 

  54. 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). This report indicates the existence of additional unknown factors in V(D)J recombination/DNA repair.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Iwasato, T., Shimizu, A., Honjo, T. & Yamagishi, H. Circular DNA is excised by immunoglobulin class switch recombination. Cell 62, 143–9 (1990).

    CAS  PubMed  Google Scholar 

  56. Matsuoka, M., Yoshida, K., Maeda, T., Usuda, S. & Sakano, H. Switch circular DNA formed in cytokine-treated mouse splenocytes: evidence for intramolecular DNA deletion in immunoglobulin class switching. Cell 62, 135–142 (1990).

    CAS  PubMed  Google Scholar 

  57. Kinoshita, K. & Honjo, T. Unique and unprecedented recombination mechanisms in class switching. Curr. Opin. Immunol. 12, 195–198 (2000).

    CAS  PubMed  Google Scholar 

  58. Manis, J. P., Dudley, D., Kaylor, L. & Alt, F. W. IgH class switch recombination to IgG1 in DNA-PKcs-deficient B cells. Immunity 16, 607–617 (2002).

    CAS  PubMed  Google Scholar 

  59. Rajewsky, K. Clonal selection and learning in the antibody system. Nature 381, 751–758 (1996).

    CAS  PubMed  Google Scholar 

  60. Frazer, J. K. et al. Identification and cloning of genes expressed by human tonsillar B lymphocyte subsets. Ann. NY Acad. Sci. 815, 316–318 (1997).

    CAS  PubMed  Google Scholar 

  61. Storb, U. et al. Somatic hypermutation of immunoglobulin genes is linked to transcription. Curr. Top. Microbiol. Immunol. 229, 11–19 (1998).

    CAS  PubMed  Google Scholar 

  62. Jacobs, H. & Bross, L. Towards an understanding of somatic hypermutation. Curr. Opin. Immunol. 13, 208–218 (2001).

    CAS  PubMed  Google Scholar 

  63. Kaartinen, M., Griffiths, G. M., Markham, A. F. & Milstein, C. mRNA sequences define an unusually restricted IgG response to 2-phenyloxazolone and its early diversification. Nature 304, 320–324 (1983).

    CAS  PubMed  Google Scholar 

  64. Liu, Y. J. et al. Within germinal centers, isotype switching of immunoglobulin genes occurs after the onset of somatic mutation. Immunity 4, 241–250 (1996).

    CAS  PubMed  Google Scholar 

  65. Bachl, J., Carlson, C., Gray-Schopfer, V., Dessing, M. & Olsson, C. Increased transcription levels induce higher mutation rates in a hypermutating cell line. J. Immunol. 166, 5051–5057 (2001).

    CAS  PubMed  Google Scholar 

  66. Betz, A. G. et al. Elements regulating somatic hypermutation of an immunoglobulin κ gene: critical role for the intron enhancer/matrix attachment region. Cell 77, 239–248 (1994).

    CAS  PubMed  Google Scholar 

  67. Fukita, Y., Jacobs, H. & Rajewsky, K. Somatic hypermutation in the heavy chain locus correlates with transcription. Immunity 9, 105–114 (1998).

    CAS  PubMed  Google Scholar 

  68. Manis, J. P. et al. Class switching in B cells lacking 3′ immunoglobulin heavy chain enhancers. J. Exp. Med. 188, 1421–1431 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Bosma, G. C. et al. DNA-dependent protein kinase activity is not required for immunoglobulin class switching. J. Exp. Med. 196, 1483–1495 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Bemark, M. et al. Somatic hypermutation in the absence of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) or recombination-activating gene (RAG)1 activity. J. Exp. Med. 192, 1509–1514 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Kenter, A. L. The liaison of isotype class switch and mismatch repair: an illegitimate affair. J. Exp. Med. 190, 307–310 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Cascalho, M., Wong, J., Steinberg, C. & Wabl, M. Mismatch repair co-opted by hypermutation. Science 279, 1207–1210 (1998).

    CAS  PubMed  Google Scholar 

  73. Schrader, C. E., Edelmann, W., Kucherlapati, R. & Stavnezer, J. Reduced isotype switching in splenic B cells from mice deficient in mismatch repair enzymes. J. Exp. Med. 190, 323–330 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Evans, E. & Alani, E. Roles for mismatch repair factors in regulating genetic recombination. Mol. Cell Biol. 20, 7839–7844 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Dominguez, O. et al. DNA polymerase μ (Polμ), homologous to TdT, could act as a DNA mutator in eukaryotic cells. EMBO J. 19, 1731–1742 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Zan, H. et al. The translesion DNA polymerase ζ plays a major role in Ig and BCL-6 somatic hypermutation. Immunity 14, 643–653 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Zeng, X. et al. DNA polymerase η is an A–T mutator in somatic hypermutation of immunoglobulin variable genes. Nature Immunol. 2, 537–541 (2001).

    CAS  Google Scholar 

  78. Faili, A. et al. Induction of somatic hypermutation in immunoglobulin genes is dependent on DNA polymerase ι. Nature 419, 944–947 (2002).

    CAS  PubMed  Google Scholar 

  79. Korthauer, U. et al. Defective expression of T-cell CD40 ligand causes X-linked immunodeficiency with hyper-IgM. Nature 361, 539–541 (1993).

    CAS  PubMed  Google Scholar 

  80. DiSanto, J. P., Bonnefoy, J. Y., Gauchat, J. F., Fischer, A. & de Saint Basile, G. CD40 ligand mutations in X-linked immunodeficiency with hyper-IgM. Nature 361, 541–543 (1993).

    CAS  PubMed  Google Scholar 

  81. Aruffo, A. et al. The CD40 ligand, gp39, is defective in activated T cells from patients with X-linked hyper-IgM syndrome. Cell 72, 291–300 (1993).

    CAS  PubMed  Google Scholar 

  82. Allen, R. C. et al. CD40 ligand gene defects responsible for X-linked hyper-IgM syndrome. Science 259, 990–993 (1993).

    CAS  PubMed  Google Scholar 

  83. Ferrari, S. et al. Mutations of CD40 gene cause an autosomal recessive form of immunodeficiency with hyper IgM. Proc. Natl Acad. Sci. USA 98, 12614–12619 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the hyper-IgM syndrome (HIGM2). Cell 102, 565–575 (2000). This paper and reference 91 show, for the first time, the role of activation-induced cytidine deaminase (AID) in class-switch recombination (CSR) and somatic hypermutation (SHM) in humans and mice, linking these two processes of antibody maturation.

    CAS  PubMed  Google Scholar 

  85. Notarangelo, L. D., Duse, M. & Ugazio, A. G. Immunodeficiency with hyper-IgM (HIM). Immunodefic. Rev. 3, 101–121 (1992).

    CAS  PubMed  Google Scholar 

  86. Zonana, J. et al. A novel X-linked disorder of immune deficiency and hypohidrotic ectodermal dysplasia is allelic to incontinentia pigmenti and due to mutations in IKK-γ (NEMO). Am. J. Hum. Genet. 67, 1555–1562 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Doffinger, R. et al. X-linked anhidrotic ectodermal dysplasia with immunodeficiency is caused by impaired NF-κB signaling. Nature Genet. 27, 277–285 (2001).

    CAS  PubMed  Google Scholar 

  88. Jain, A. et al. Specific missense mutations in NEMO result in hyper-IgM syndrome with hypohydrotic ectodermal dysplasia. Nature Immunol. 2, 223–228 (2001).

    CAS  Google Scholar 

  89. Durandy, A. et al. Abnormal CD40-mediated activation pathway in B lymphocytes from patients with hyper-IgM syndrome and normal CD40 ligand expression. J. Immunol. 158, 2576–2584 (1997).

    CAS  PubMed  Google Scholar 

  90. Minegishi, Y. et al. Mutations in activation-induced cytidine deaminase in patients with hyper IgM syndrome. Clin. Immunol. 97, 203–210 (2000).

    CAS  PubMed  Google Scholar 

  91. Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102, 553–563 (2000).

    CAS  PubMed  Google Scholar 

  92. Muramatsu, M. et al. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J. Biol. Chem. 274, 18470–18476 (1999).

    CAS  PubMed  Google Scholar 

  93. Faili, A. et al. AID-dependent somatic hypermutation occurs as a DNA single-strand event in the BL2 cell line. Nature Immunol. 3, 815–821 (2002).

    CAS  Google Scholar 

  94. Nagaoka, H., Muramatsu, M., Yamamura, N., Kinoshita, K. & Honjo, T. Activation-induced deaminase (AID)-directed hypermutation in the immunoglobulin Sμ region: implication of AID involvement in a common step of class switch recombination and somatic hypermutation. J. Exp. Med. 195, 529–534 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Yoshikawa, K. et al. AID enzyme-induced hypermutation in an actively transcribed gene in fibroblasts. Science 296, 2033–2036 (2002).

    CAS  PubMed  Google Scholar 

  96. Okazaki, I. M., Kinoshita, K., Muramatsu, M., Yoshikawa, K. & Honjo, T. The AID enzyme induces class switch recombination in fibroblasts. Nature 416, 340–345 (2002).

    CAS  PubMed  Google Scholar 

  97. Arakawa, H., Hauschild, J. & Buerstedde, J. M. Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science 295, 1301–1306 (2002).

    CAS  PubMed  Google Scholar 

  98. Hein, K. et al. Processing of switch transcripts is required for targeting of antibody class switch recombination. J. Exp. Med. 188, 2369–2374 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Wiesendanger, M., Scharff, M. D. & Edelmann, W. Somatic hypermutation, transcription, and DNA mismatch repair. Cell 94, 415–418 (1998).

    CAS  PubMed  Google Scholar 

  100. Kong, Q. & Maizels, N. DNA breaks in hypermutating immunoglobulin genes: evidence for a break-and-repair pathway of somatic hypermutation. Genetics 158, 369–378 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Sale, J. E. & Neuberger, M. S. TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line. Immunity 9, 859–869 (1998).

    CAS  PubMed  Google Scholar 

  102. Wuerffel, R. A., Du, J., Thompson, R. J. & Kenter, A. L. IgSγ3 DNA-specifc double strand breaks are induced in mitogen-activated B cells and are implicated in switch recombination. J. Immunol. 159, 4139–4144 (1997).

    CAS  PubMed  Google Scholar 

  103. Bross, L. et al. DNA double-strand breaks in immunoglobulin genes undergoing somatic hypermutation. Immunity 13, 589–597 (2000).

    CAS  PubMed  Google Scholar 

  104. Papavasiliou, F. N. & Schatz, D. G. Cell-cycle-regulated DNA double-stranded breaks in somatic hypermutation of immunoglobulin genes. Nature 408, 216–221 (2000).

    CAS  PubMed  Google Scholar 

  105. Petersen, S. et al. AID is required to initiate Nbs1/γ-H2AX focus formation and mutations at sites of class switching. Nature 414, 660–665 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Rolink, A. Mε heavy chain class switching. Immunity 5, 319–330 (1996).

    CAS  PubMed  Google Scholar 

  107. Casellas, R. et al. Ku80 is required for immunoglobulin isotype switching. EMBO J. 17, 2404–2411 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Chen, X., Kinoshita, K. & Honjo, T. Variable deletion and duplication at recombination junction ends: implication for staggered double-strand cleavage in class-switch recombination. Proc. Natl Acad. Sci. USA 98, 13860–13865 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Doi, T., Kinoshita, K., Ikegawa, M., Muramatsu, M. & Honjo, T. De novo protein synthesis is required for the activation-induced cytidine deaminase function in class-switch recombination. Proc. Natl Acad. Sci. USA 100, 2634–2638 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Petersen-Mahrt, S. K., Harris, R. S. & Neuberger, M. S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418, 99–104 (2002).

    CAS  PubMed  Google Scholar 

  111. Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc. Natl Acad. Sci. USA 100, 4102–4107 (2003). This paper shows the action of AID on single-stranded DNA.

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Chaudhuri, J. et al. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 422, 726–730 (2003).

    CAS  PubMed  Google Scholar 

  113. Ramiro, A. R., Stavropoulos, P., Jankovic, M. & Nussenzweig, M. C. Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand. Nature Immunol. 4, 452–456 (2003).

    CAS  Google Scholar 

  114. Shinkura, R. et al. The influence of transcriptional orientation on endogenous switch region function. Nature Immunol. 4, 435–441 (2003). References 112–114 describe the activity of AID on the non-transcribed single-stranded DNA.

    CAS  Google Scholar 

  115. Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10, 1247–1253 (2002).

    CAS  PubMed  Google Scholar 

  116. Yu, K., Chedin, F., Hsieh, C. L., Wilson, T. E. & Lieber, M. R. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nature Immunol. 4, 442–451 (2003). This paper indicates that the formation of RNA–DNA hybrids during transcription leads to R-loops and that cytosine residues on single-stranded DNA become targets for AID.

    CAS  Google Scholar 

  117. Fugmann, S. D. & Schatz, D. G. RNA AIDS DNA. Nature Immunol. 4, 429–430 (2003).

    CAS  Google Scholar 

  118. Rada, C. et al. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr. Biol. 12, 1748–1755 (2002). This description of the immunological phenotype of uracil N -glycosylase (Ung)-deficient mice supports the hypothesis of AID as a DNA-editing enzyme.

    CAS  PubMed  Google Scholar 

  119. Imai, K. et al. Hyper-IgM syndrome type 4 with a B-lymphocyte intrinsic selective deficiency in immunoglobulin class switch recombination. J. Clin. Immunol. 112, 136–142 (2003).

    CAS  Google Scholar 

  120. Kinzler, K. W. & Vogelstein, B. Cancer-susceptibility genes. Gatekeepers and caretakers. Nature 386, 761–763 (1997).

    CAS  PubMed  Google Scholar 

  121. 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 

  122. Ferguson, D. O. & Alt, F. W. DNA double strand break repair and chromosomal translocation: lessons from animal models. Oncogene 20, 5572–5579 (2001). A review of the mouse models that show the 'genome caretaker' role of non-homologous end-joining (NHEJ) factors.

    CAS  PubMed  Google Scholar 

  123. Difilippantonio, M. J. et al. Evidence for replicative repair of DNA double-strand breaks leading to oncogenic translocation and gene amplification. J. Exp. Med. 196, 469–480 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Zhu, C. et al. Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocation. Cell 109, 811–821 (2002).

    CAS  PubMed  Google Scholar 

  125. Rooney, S. et al. Defective DNA repair and increased genomic instability in Artemis-deficient murine cells. J. Exp. Med. 197, 553–565 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. 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). The authors show that partial Artemis deficiency in humans can cause B-cell lymphoma, indicating a genome caretaker role for Artemis.

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Nelms, K. A. & Goodnow, C. C. Genome-wide ENU mutagenesis to reveal immune regulators. Immunity 15, 409–418 (2001).

    CAS  PubMed  Google Scholar 

  128. Noordzij, J. G. et al. The immunophenotypic and immunogenotypic B-cell differentiation arrest in bone marrow of RAG-deficient SCID patients corresponds to residual recombination activities of mutated RAG proteins. Blood 100, 2145–2152 (2002).

    CAS  PubMed  Google Scholar 

  129. Imai, K. et al. Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nature Immunol. 4, 1023–1028 (2003).

    CAS  Google Scholar 

Download references

Acknowledgements

We thank F. Alt for his permission to refer to unpublished data. This work was supported by institutional grants from Institut National de la Santé et de la Recherche Médicale (INSERM) and from Ministère de la Recherche et de la Technologie as well as grants from Commissariat à l'Energie Atomique, Association de Recherche sur le Cancer and the Louis Jeantet Fundation.

Author information

Authors and Affiliations

  1. Dévelopement Normal et Pathologique du Système Immunitaire (INSERM U429), Hôpital Necker Enfants Malades, 149 rue de Sèvres, Paris, 75015, France

    Jean-Pierre de Villartay, Alain Fischer & Anne Durandy

Authors
  1. Jean-Pierre de Villartay
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alain Fischer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anne Durandy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jean-Pierre de Villartay.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

LocusLink

AID

APOBEC1

Artemis

CD40

CD40L

HIGM2

HIGM4

Ku70

Ku80

MRE11

NBS1

RAD50

RAG1

RAG2

OMIM

NBS

Glossary

SOMATIC HYPERMUTATION

Mutations occurring with high frequency in the V region of immunoglobulin genes, followed by positive selection of B cells.

GERMINAL CENTRES

Lymphoid formations in secondary lymphoid organs that are formed by B-cell proliferation after antigen stimulation. CSR and SHM occur inside the germinal centres.

T-B-SCID

T-B-SCID patients are characterized by an absence of B and T cells, but natural-killer cells are present. They represent about 20% of all cases of SCID. T-B-SCID is caused by mutations in RAG1, RAG2 or Artemis.

RECOMBINATION SIGNAL SEQUENCES

(RSSs). Composed of conserved heptamers and nonamers separated by 12 or 23 base-pair spacers that flank all of the V, D and J region genes and serve as the recognition target for the RAG1 and RAG2 proteins.

NHEJ PATHWAY

DNA damage can be repaired by two different mechanisms: homologous recombination (HR) or non-homologous end-joining (NHEJ). The DNA double-strand breaks that occur during V(D)J recombination are repaired through NHEJ.

HYPOMORPHIC MUTATIONS

Mutations are considered hypomorphic when they do not result in a complete loss of function. Study of these mutations is sometimes the only way to link a disease to a particular gene defect when the complete loss of function is embryonic lethal (for example, DNA ligase IV).

GRAFT-VERSUS-HOST DISEASE

(GVHD). The immune reaction that results from injection of allogenic T cells into an immunodeficient animal or human that is incapable of mediating graft rejection. One of the characteristics of GVHD is infiltration of tissues (skin, gut) by activated, reactive T cells.

NIJMEGEN BREAKAGE SYNDROME

(NBS). A rare human inherited disorder that is characterized by developmental defects, microcephaly, immune deficiency and a high incidence of cancer. Patients with NBS are sensitive to various agents that cause DNA double-strand breaks. Mutations in the nibrin/NBS1 gene are responsible for NBS. NBS1 is one of the components of the MRE11–NBS1–RAD50 complex (NMR complex).

COMPLEMENTARITY-DETERMINING REGION

(CDR). The hypervariable regions of an antibody molecule, consisting of three loops from the heavy chain and three from the light chain, that together form the antigen-binding site.

Rights and permissions

Reprints and permissions

About this article

Cite this article

de Villartay, JP., Fischer, A. & Durandy, A. The mechanisms of immune diversification and their disorders. Nat Rev Immunol 3, 962–972 (2003). https://doi.org/10.1038/nri1247

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nri1247

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