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Somatic hypermutations

Professeurs Marie-Paule LEFRANC et Gérard LEFRANC

Université Montpellier II et Laboratoire d'ImmunoGénétique Moléculaire, LIGM, UPR CNRS 1142, Institut de Génétique Humaine,
141 rue de la Cardonille, 34396 Montpellier Cedex 5 (France)
Tel. : +33 (0)4 34 35 99 65 - Fax : +33 (0)4 34 35 99 01
E-mail Marie-Paule.Lefranc@igh.cnrs.fr, IMGT: http://www.imgt.org

SUMMARY

  1. Definition
  2. Polymerase η hotspots
  3. Polymerase κ hotspots
  4. Activation-induced deaminase (AID)
  5. Mutability index
  6. Mutational strand bias in human IGLV genes
  7. Mutability of G and C bases within targeting motifs
  8. References


  1. Definition

    Somatic hypermutation (SHM) is the mechanism which diversifies the immunoglobulin (IG) repertoire by introducing mutations into rearranged IG V genes. SHM occurs in B cells that undergo clonal expansion during T cell-dependent responses in germinal center. SHM is dependent on the expression of activation-induced cytidine deaminase (AID). Hypermutagenesis is characterized by the frequent occurrence of point mutations within V region DNA segments that are 1000-2000 bp long.

  2. Polymerase η hotspots

    Polymerase η hotspots [6] include:

  3. Polymerase κ hotspots

    Human polymerase κ (an error - prone polymerase) shares the A/GGC/TA/T (RGYW) and A/TA (WA) hotspots with polymerase η, but not the minor hotspot in TA or TA/T(TW).

  4. Activation-induced deaminase (AID)

    SHM, class switch recombination (CSR) [7, 8], and gene conversion [9] require activation-induced cytidine deaminase (AID).
    Owing to its structural homology with the RNA editing enzyme Apobec-1, it has initially been proposed that AID might edit RNA resulting in the production of a mutator protein. However, data are in support of AID being a DNA mutator [10-18].

    AID catalyses the deamination of C to U in DNA, generating mutations at C bases. AID deaminates deoxycytidine to deoxyuridine in single-stranded DNA (ssDNA), and the ssDNA is thought to be generated during transcription, when the DNA strands are separated within the transcription bubble. This mutagenic event is targeted to actively transcribed sequences. In vitro models have suggested that the non-transcribed strand is the preferred target for deamination [10-18]. However in human IGLV, 92% of mutations of G occur in GNA/T (GNW) motifs, these hotspots are often independent of C. This suggests that mutations from G arise independent of C on the non-transcribed strand. If cell division follows deamination, the resulting mismatch will be repaired producing a C to T transition. However if U is removed by uracil DNA-glycosylase, this would generate an abasic lesion, which could be repaired on cell divison by the introduction of A, C, G, or T by a DNA polymerase [10].

  5. Mutability index

    The mutatibility index is the observed number of point mutations (base substitutions) from a specified nucleotide within a particular 3 or 4 base motif divided by the expected number of point mutations from a given base within the motif [19]. The expected number of base substitutions from a given base within a particular motif is computed as follows:

    Comparison of base substitution frequencies was performed, in [20], using a Mann-Whitney U-test with Microstat software.

  6. Mutational strand bias in human IGLV genes

    Unusually, in human IGLV genes, there is G•C strand bias favoring mutation from G. In IGLV, 92% of mutations from G occur in GNW motifs [20]. Mutations from G arise independent of C suggesting that both DNA strands are deaminated and that the transcribed strand is preferentially deaminated in human IGLV resulting in bias towards mutations from G [20].
    In IGHV genes in vivo, RGYW/WRCY and the motifs contained within them such as GC and AGY are preferred targets for SHM [19, 21-24]. All motifs which favor mutation from G and C are reverse complement but not palindromic, leading to the proposition that both DNA strands are hypermutation targets [24, 25]. In IGHV, there is no G•C strand bias and hotspots for mutation of G or C often involve GC motifs [19, 21, 26]. Consequently it is not possible to discriminate between two possibilities:

    In human IGLV, there is G•C strand bias [26]. Mutation of G in human IGLV genes is dependent on local microsequence but not necessarily associated with C on the non-transcribed strand. These data support the hypothesis that mutations from G and C occur as a result of targeted AID activity on both DNA strands, favoring deamination of the transcribed strand in human IGLV genes [20].

  7. Mutability of G and C bases within targeting motifs

  8. References:
    [1] Storb, U. Curr. Opin. Immunol. 8, 206-214 (1996).
    [2] Papavasiliou, F. N. and Schatz, D. G. Nature, 408, 216-221 (2000).
    [3] Bross, L. et al. Immunity, 13,589-597 (2000).
    [4] Betz, A. G. et al. PNAS. 90, 2385-2388 (1993).
    [5] Shapiro, G. et al. J. Immunol. 163, 259-268 (1999).
    [6] Rogozin, I. B. et al. Nature Immunology, 2, 530-536 (2001).
    [7] Muramatsu, M. et al. Cell, 102, 553-563 (2000).
    [8] Revy, P. Cell, 102, 565-575 (2000).
    [9] Anakawa, H. et al. Science, 15, 1301-1306 (2002).
    [10] Petersen-Mahrt, S. K. et al. Nature, 418, 99-103 (2002).
    [11] Di Noia, J. and Neuberger, M. S. Nature, 419, 43-48 (2002).
    [12] Faili, A. et al. Nat. Immunol. 3, 815-821 (2002).
    [13] Pham, P. et al. Nature, 424, 103-107 (2003).
    [14] Dickerson, S. K. et al. J. Exp. Med. 197, 1291-1296 (2003).
    [15] Chaudhuri, J. et al. Nature, 422, 726-730 (2003).
    [16] Sohail, A. et al. Nucleic Acids Res. 31, 2990-2994 (2003).
    [17] Ramiro, A. R. et al. Nat. Immunol. 4, 452-456 (2003).
    [18] Bransteitter, R. et al. Proc. Natl. Acad. Sci. USA, 100, 4102-4107 (2003).
    [19] Smith, D. S. et al. J. Immunol. 156, 2642-2652 (1996).
    [20] Boursier, L. et al. Mol. Immunol. 40, 1273-1278 (2004).
    [21] Spencer, J. et al. J. Immunol. 162, 6596-6601 (1999).
    [22] Shapiro, G. S. et al. Mol. Immunol. 40,287-295 (2003).
    [23] Rogozin, I. B. and Kolchanov, N. A. Biochim. Biophys. Acta. 1171, 11-18 (1992).
    [24] Milstein, C. et al. Proc. Natl. Acad. Sci. USA,95, 8791-8794 (1998).
    [25] Dunn-Walters, D. K. et al. J. Immunol. 160, 2360-2364 (1998).
    [26] Boursier, L. et al. Mol. Immunol. 39, 1025-1034 (2003).


Created: Monday, 11-Jul-2011 12:57:02 CEST
Authors: Gérard Lefranc and Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr
Editors: Ruth Henry, Chantal Ginestoux

Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Res., 27:209-212 (1999); doi: 10.1093/nar/27.1.209 Full text Cover; Ruiz, M. et al., Nucleic Acids Res., 28:219-221 (2000); doi: 10.1093/nar/28.1.219 Full text; Lefranc, M.-P., Nucleic Acids Res., 29:207-209 (2001); doi: 10.1093/nar/29.1.207 Full text; Lefranc, M.-P., Nucleic Acids Res., 31:307-310 (2003); doi: 10.1093/nar/gkg085 Full text; Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5:45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33:D593-597 (2005); doi: 10.1093/nar/gki065 Full text; Lefranc, M.-P. et al., Nucleic Acids Res., 37:D1006-1012 (2009); doi: 10.1093/nar/gkn838 Full text; Lefranc, M.-P. et al., Nucleic Acids Res., 43:D413-422 (2015); doi: 10.1093/nar/gku1056 Full text.
For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

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