Skip to main content
Log in

Controlling somatic hypermutation in immunoglobulin variable and switch regions

  • Published:
Immunologic Research Aims and scope Submit manuscript

Abstract

Activation-induced deaminase (AID) is a B-cell-specific enzyme required for initiating the mechanisms of affinity maturation and isotype switching of antibodies. AID functions by deaminating cytosine to uracil in DNA, which initiates a cascade of events resulting in mutations and strand breaks in the immunoglobulin loci. There is an intricate interplay between faithful DNA repair and mutagenic DNA repair during somatic hypermutation, in that some proteins from accurate repair pathways are also involved in mutagenesis. One factor that shifts the balance from faithful to mutagenic repair is the genomic sequence of the switch regions. Indeed, the sequence of the switch μ region is designed to maximize AID access to increase the abundance of clustered dU bases. The frequency and proximity of these dU nucleotides then in turn inhibit faithful repair and promote strand breaks.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell. 2000;102:553–63.

    Article  PubMed  CAS  Google Scholar 

  2. Revy P, Muto T, Levy Y, Geissmann F, Plebani A, Sanal O, et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell. 2000;102:565–75.

    Article  PubMed  CAS  Google Scholar 

  3. Arakawa H, Hauschild J, Buerstedde JM. Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science. 2002;295:1301–6.

    Article  PubMed  CAS  Google Scholar 

  4. Petersen-Mahrt SK, Harris RS, Neuberger MS. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature. 2002;418:99–103.

    Article  PubMed  CAS  Google Scholar 

  5. Di Noia J, Neuberger MS. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase. Nature. 2002;419:43–8.

    Article  PubMed  CAS  Google Scholar 

  6. Rada C, Williams GT, Nilsen H, Barnes DE, Lindahl T, Neuberger MS. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr Biol. 2002;12:1748–55.

    Article  PubMed  CAS  Google Scholar 

  7. Pham P, Bransteitter R, Petruska J, Goodman MF. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature. 2003;424:103–7.

    Article  PubMed  CAS  Google Scholar 

  8. Yu K, Chedin F, Hsieh CL, Wilson TE, Lieber MR. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol. 2003;4:442–51.

    Article  PubMed  CAS  Google Scholar 

  9. Zarrin AA, Alt FW, Chaudhuri J, Stokes N, Kaushal D, Du PL, et al. An evolutionarily conserved target motif for immunoglobulin class-switch recombination. Nat Immunol. 2004;5:1275–81.

    Article  PubMed  CAS  Google Scholar 

  10. Martomo SA, Yang WW, Gearhart PJ. A role for Msh6 but not Msh3 in somatic hypermutation and class switch recombination. J Exp Med. 2004;200:61–8.

    Article  PubMed  CAS  Google Scholar 

  11. Barreto V, Reina-San-Martin B, Ramiro AR, McBride KM, Nussenzweig MC. C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion. Mol Cell. 2003;12:501–8.

    Article  PubMed  CAS  Google Scholar 

  12. Imai K, Slupphaug G, Lee WI, Revy P, Nonoyama S, Catalan N, et al. Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nat Immunol. 2003;4:1023–8.

    Article  PubMed  CAS  Google Scholar 

  13. Ross AL, Sale JE. The catalytic activity of REV1 is employed during immunoglobulin gene diversification in DT40. Mol Immunol. 2006;43:1587–94.

    Article  PubMed  CAS  Google Scholar 

  14. Jansen JG, Langerak P, Tsaalbi-Shtylik A, van den Berk P, Jacobs H, de Wind N. Strand-biased defect in C/G transversions in hypermutating immunoglobulin genes in Rev1-deficient mice. J Exp Med. 2006;203:319–23.

    Article  PubMed  Google Scholar 

  15. Guikema JE, Linehan EK, Tsuchimoto D, Nakabeppu Y, Strauss PR, Stavnezer J, et al. APE1- and APE2-dependent DNA breaks in immunoglobulin class switch recombination. J Exp Med. 2007;204:3017–26.

    Article  PubMed  CAS  Google Scholar 

  16. Winter DB, Phung QH, Umar A, Baker SM, Tarone RE, Tanaka K, et al. Altered spectra of hypermutation in antibodies from mice deficient for the DNA mismatch repair protein PMS2. Proc Natl Acad Sci USA. 1998;95:6953–8.

    Article  PubMed  CAS  Google Scholar 

  17. Frey S, Bertocci B, Delbos F, Quint L, Weill JC, Reynaud CA. Mismatch repair deficiency interferes with the accumulation of mutations in chronically stimulated B cells and not with the hypermutation process. Immunity. 1998;9:127–34.

    Article  PubMed  CAS  Google Scholar 

  18. Phung QH, Winter DB, Alrefai R, Gearhart PJ. Hypermutation in Ig V genes from mice deficient in the MLH1 mismatch repair protein. J Immunol. 1999;162:3121–4.

    PubMed  CAS  Google Scholar 

  19. Kim N, Bozek G, Lo JC, Storb U. Different mismatch repair deficiencies all have the same effects on somatic hypermutation: intact primary mechanism accompanied by secondary modifications. J Exp Med. 1999;190:21–30.

    Article  PubMed  CAS  Google Scholar 

  20. Wiesendanger M, Kneitz B, Edelmann W, Scharff MD. Somatic hypermutation in MutS homologue (MSH)3-, MSH6-, and MSH3/MSH6-deficient mice reveals a role for the MSH2-MSH6 heterodimer in modulating the base substitution pattern. J Exp Med. 2000;191:579–84.

    Article  PubMed  CAS  Google Scholar 

  21. Ehrenstein MR, Rada C, Jones AM, Milstein C, Neuberger MS. Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination. Proc Natl Acad Sci USA. 2001;98:14553–8.

    Article  PubMed  CAS  Google Scholar 

  22. Li Z, Scherer SJ, Ronai D, Iglesias-Ussel MD, Peled JU, Bardwell PD, et al. Examination of Msh6- and Msh3-deficient mice in class switching reveals overlapping and distinct roles of MutS homologues in antibody diversification. J Exp Med. 2004;200:47–59.

    Article  PubMed  CAS  Google Scholar 

  23. Phung QH, Winter DB, Cranston A, Tarone RE, Bohr VA, Fishel R, et al. Increased hypermutation at G and C nucleotides in immunoglobulin variable genes from mice deficient in the MSH2 mismatch repair protein. J Exp Med. 1998;187:1745–51.

    Article  PubMed  CAS  Google Scholar 

  24. Rada C, Ehrenstein MR, Neuberger MS, Milstein C. Hot spot focusing of somatic hypermutation in MSH2-deficient mice suggests two stages of mutational targeting. Immunity. 1998;9:135–41.

    Article  PubMed  CAS  Google Scholar 

  25. Bardwell PD, Woo CJ, Wei K, Li Z, Martin A, Sack SZ, et al. Altered somatic hypermutation and reduced class-switch recombination in exonuclease 1-mutant mice. Nat Immunol. 2004;5:224–9.

    Article  PubMed  CAS  Google Scholar 

  26. McDonald JP, Frank EG, Plosky BS, Rogozin IB, Masutani C, Hanaoka F, et al. 129-derived strains of mice are deficient in DNA polymerase iota and have normal immunoglobulin hypermutation. J Exp Med. 2003;198:635–43.

    Article  PubMed  CAS  Google Scholar 

  27. Martomo SA, Yang WW, Vaisman A, Maas A, Yokoi M, Hoeijmakers JH, et al. Normal hypermutation in antibody genes from congenic mice defective for DNA polymerase iota. DNA Repair (Amst). 2006;5:392–8.

    Article  CAS  Google Scholar 

  28. Schenten D, Gerlach VL, Guo C, Velasco-Miguel S, Hladik CL, White CL, et al. DNA polymerase kappa deficiency does not affect somatic hypermutation in mice. Eur J Immunol. 2002;32:3152–60.

    Article  PubMed  CAS  Google Scholar 

  29. Bertocci B, De Smet A, Flatter E, Dahan A, Bories JC, Landreau C, et al. Cutting edge: DNA polymerases mu and lambda are dispensable for Ig gene hypermutation. J Immunol. 2002;168:3702–6.

    PubMed  CAS  Google Scholar 

  30. Masuda K, Ouchida R, Hikida M, Kurosaki T, Yokoi M, Masutani C, et al. DNA polymerases eta and theta function in the same genetic pathway to generate mutations at A/T during somatic hypermutation of Ig genes. J Biol Chem. 2007;282:17387–94.

    Article  PubMed  CAS  Google Scholar 

  31. Martomo SA, Saribasak H, Yokoi M, Hanaoka F, Gearhart PJ. Reevaluation of the role of DNA polymerase theta in somatic hypermutation of immunoglobulin genes. DNA Repair (Amst). 2008;7:1603–8.

    Article  CAS  Google Scholar 

  32. Schenten D, Kracker S, Esposito G, Franco S, Klein U, Murphy M, et al. Pol zeta ablation in B cells impairs the germinal center reaction, class switch recombination, DNA break repair, and genome stability. J Exp Med. 2009;206:477–90.

    Article  PubMed  CAS  Google Scholar 

  33. Zeng X, Winter DB, Kasmer C, Kraemer KH, Lehmann AR, Gearhart PJ. DNA polymerase eta is an A-T mutator in somatic hypermutation of immunoglobulin variable genes. Nat Immunol. 2001;2:537–41.

    Article  PubMed  CAS  Google Scholar 

  34. Delbos F, De Smet A, Faili A, Aoufouchi S, Weill JC, Reynaud CA. Contribution of DNA polymerase eta to immunoglobulin gene hypermutation in the mouse. J Exp Med. 2005;201:1191–6.

    Article  PubMed  CAS  Google Scholar 

  35. Martomo SA, Yang WW, Wersto RP, Ohkumo T, Kondo Y, Yokoi M, et al. Different mutation signatures in DNA polymerase eta- and MSH6-deficient mice suggest separate roles in antibody diversification. Proc Natl Acad Sci USA. 2005;102:8656–61.

    Article  PubMed  CAS  Google Scholar 

  36. Delbos F, Aoufouchi S, Faili A, Weill JC, Reynaud CA. DNA polymerase eta is the sole contributor of A/T modifications during immunoglobulin gene hypermutation in the mouse. J Exp Med. 2007;204:17–23.

    Article  PubMed  CAS  Google Scholar 

  37. Faili A, Aoufouchi S, Weller S, Vuillier F, Stary A, Sarasin A, et al. DNA polymerase eta is involved in hypermutation occurring during immunoglobulin class switch recombination. J Exp Med. 2004;199:265–70.

    Article  PubMed  CAS  Google Scholar 

  38. Zeng X, Negrete GA, Kasmer C, Yang WW, Gearhart PJ. Absence of DNA polymerase eta reveals targeting of C mutations on the nontranscribed strand in immunoglobulin switch regions. J Exp Med. 2004;199:917–24.

    Article  PubMed  CAS  Google Scholar 

  39. Wilson TM, Vaisman A, Martomo SA, Sullivan P, Lan L, Hanaoka F, et al. MSH2-MSH6 stimulates DNA polymerase eta, suggesting a role for A:T mutations in antibody genes. J Exp Med. 2005;201:637–45.

    Article  PubMed  CAS  Google Scholar 

  40. Ramiro AR, Jankovic M, Eisenreich T, Difilippantonio S, Chen-Kiang S, Muramatsu M, et al. AID is required for c-myc/IgH chromosome translocations in vivo. Cell. 2004;118:431–8.

    Article  PubMed  CAS  Google Scholar 

  41. Unniraman S, Zhou S, Schatz DG. Identification of an AID-independent pathway for chromosomal translocations between the Igh switch region and Myc. Nat Immunol. 2004;5:1117–23.

    Article  PubMed  CAS  Google Scholar 

  42. Takizawa M, Tolarova H, Li Z, Dubois W, Lim S, Callen E, et al. AID expression levels determine the extent of cMyc oncogenic translocations and the incidence of B cell tumor development. J Exp Med. 2008;205:1949–57.

    Article  PubMed  CAS  Google Scholar 

  43. Nilsen H, Stamp G, Andersen S, Hrivnak G, Krokan HE, Lindahl T, et al. Gene-targeted mice lacking the Ung uracil-DNA glycosylase develop B-cell lymphomas. Oncogene. 2003;22:5381–6.

    Article  PubMed  CAS  Google Scholar 

  44. Okazaki IM, Hiai H, Kakazu N, Yamada S, Muramatsu M, Kinoshita K, et al. Constitutive expression of AID leads to tumorigenesis. J Exp Med. 2003;197:1173–81.

    Article  PubMed  CAS  Google Scholar 

  45. Lebecque SG, Gearhart PJ. Boundaries of somatic mutation in rearranged immunoglobulin genes: 5’ boundary is near the promoter, and 3’ boundary is approximately 1 kb from V(D)J gene. J Exp Med. 1990;172:1717–27.

    Article  PubMed  CAS  Google Scholar 

  46. Xue K, Rada C, Neuberger MS. The in vivo pattern of AID targeting to immunoglobulin switch regions deduced from mutation spectra in msh2-/- ung-/- mice. J Exp Med. 2006;203:2085–94.

    Article  PubMed  CAS  Google Scholar 

  47. Peters A, Storb U. Somatic hypermutation of immunoglobulin genes is linked to transcription initiation. Immunity. 1996;4:57–65.

    Article  PubMed  CAS  Google Scholar 

  48. Conticello SG, Ganesh K, Xue K, Lu M, Rada C, Neuberger MS. Interaction between antibody-diversification enzyme AID and spliceosome-associated factor CTNNBL1. Mol Cell. 2008;31:474–84.

    Article  PubMed  CAS  Google Scholar 

  49. Nambu Y, Sugai M, Gonda H, Lee CG, Katakai T, Agata Y, et al. Transcription-coupled events associating with immunoglobulin switch region chromatin. Science. 2003;302:2137–40.

    Article  PubMed  CAS  Google Scholar 

  50. Reina-San-Martin B, Difilippantonio S, Hanitsch L, Masilamani RF, Nussenzweig A, Nussenzweig MC. H2AX is required for recombination between immunoglobulin switch regions but not for intra-switch region recombination or somatic hypermutation. J Exp Med. 2003;197:1767–78.

    Article  PubMed  CAS  Google Scholar 

  51. Huang FT, Yu K, Balter BB, Selsing E, Oruc Z, Khamlichi AA, et al. Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region. Mol Cell Biol. 2007;27:5921–32.

    Article  PubMed  CAS  Google Scholar 

  52. Rajagopal D, Maul RW, Ghosh A, Chakraborty T, Khamlichi AA, Sen R, et al. Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutation. J Exp Med. 2009;206:1237–44.

    Article  PubMed  CAS  Google Scholar 

  53. Kothapalli N, Norton DD, Fugmann SD. Cutting edge: a cis-acting DNA element targets AID-mediated sequence diversification to the chicken Ig light chain gene locus. J Immunol. 2008;180:2019–23.

    PubMed  CAS  Google Scholar 

  54. Blagodatski A, Batrak V, Schmidl S, Schoetz U, Caldwell RB, Arakawa H, et al. A cis-acting diversification activator both necessary and sufficient for AID-mediated hypermutation. PLoS Genet. 2009;5:e1000332.

    Article  PubMed  CAS  Google Scholar 

  55. Kim Y, Tian M. NF-kappaB family of transcription factor facilitates gene conversion in chicken B cells. Mol Immunol. 2009;46:3283–91.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by the Intramural Research Program of the NIH, National Institute on Aging.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Patricia J. Gearhart.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Maul, R.W., Gearhart, P.J. Controlling somatic hypermutation in immunoglobulin variable and switch regions. Immunol Res 47, 113–122 (2010). https://doi.org/10.1007/s12026-009-8142-5

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12026-009-8142-5

Keywords

Navigation