Abstract
Mutational spectra analysis of 15 immunoglobulin genes suggested that consensus motifs RGYW and WA were universal descriptors of somatic hypermutation. Highly mutable sites, “hotspots”, that matched WA were preferentially found in one DNA strand and RGYW hotspots were found in both strands. Analysis of base-substitution hotspots in DNA polymerase error spectra showed that 33 of 36 hotspots in the human polymerase η spectrum conformed to the WA consensus. This and four other characteristics of polymerase η substitution specificity suggest that errors introduced by this enzyme during synthesis of the nontranscribed DNA strand in variable regions may contribute to strand-specific somatic hypermutagenesis of immunoglobulin genes at A-T base pairs.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Neuberger, M. S. & Milstein, C. Somatic hypermutation. Curr. Opin. Immunol. 7, 248–254 (1995).
Jacobs, H. & Bross, L. Towards an understanding of somatic hypermutation. Curr. Opin. Immunol. 13, 208–218 (2001).
Lebecque, S. G. & Gearhart, P. J. 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. 172, 1717–1727 (1990).
Berek, C. & Milstein, C. Mutation drift and repertoire shift in the maturation of the immune response. Immunol. Rev. 96, 23–41 (1987).
Rogozin, I. B. & Kolchanov, N. A. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. Biochim. Biophys. Acta 1171, 11–18 (1992).
Reynaud, C. A., Garcia, C., Hein, W. R. & Weill, J. C. Hypermutation generating the sheep immunoglobulin repertoire is an antigen-independent process. Cell 80, 115–125 (1995).
Rogozin, I. B., Sredneva, N. E. & Kolchanov, N. A. Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus. Biochim. Biophys. Acta 1306, 171–178 (1996).
Hsu, E. Mutation, selection, and memory in B lymphocytes of exothermic vertebrates. Immunol. Rev. 162, 25–36 (1998).
Goyenechea, B. & Milstein, C. Modifying the sequence of an immunoglobulin V-gene alters the resulting pattern of hypermutation. Proc. Natl Acad. Sci. USA 93, 13979–13984 (1996).
Klix, N. et al. Multiple sequences from downstream of the Jκ cluster can combine to recruit somatic hypermutation to a heterologous, upstream mutation domain. Eur. J. Immunol. 28, 317–326 (1998).
Bachl, J., Steinberg, C. & Wabl, M. Critical test of hot spot motifs for immunoglobulin hypermutation. Eur. J. Immunol. 27, 3398–3403 (1997).
Rajewsky, K. Clonal selection and learning in the antibody system. Nature 381, 751–758 (1996).
Wagner, S. D., Milstein, C. & Neuberger, M. S. Codon bias targets mutation. Nature 376, 732 (1995).
Shapiro, G. S., Aviszus, K., Ikle, D. & Wysocki, L. J. Predicting regional mutability in antibody V genes based solely on di- and trinucleotide sequence composition. J. Immunol. 163, 259–268 (1999).
Milstein, C., Neuberger, M. S. & Staden, R. Both DNA strands of antibody genes are hypermutation targets. Proc. Natl Acad. Sci. USA 95, 8791–8794 (1998).
Foster, S. J., Dorner, T. & Lipsky, P. E. Somatic hypermutation of VκJκ rearrangements: targeting of RGYW motifs on both DNA strands and preferential selection of mutated codons within RGYW motifs. Eur. J. Immunol. 29, 4011–4021 (1999).
Bross, L. et al. DNA double-strand breaks in immunoglobulin genes undergoing somatic hypermutation. Immunity 13, 589–597 (2000).
Papavasiliou, F. N. & Schatz, D. G. Cell-cycle-regulated DNA double-stranded breaks in somatic hypermutation of immunoglobulin genes. Nature 408, 216–221 (2000).
Weber, J. S., Berry, J., Manser, T. & Claflin, J. L. Position of the rearranged Vκ and its 5′ flanking sequences determines the location of somatic mutations in the Jκ locus. J. Immunol. 146, 3652–3655 (1991).
Smith, D. S. et al. Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells. J. Immunol. 156, 2642–2652 (1996).
Both, G. W., Taylor, L., Pollard, J. W. & Steele, E. J. Distribution of mutations around rearranged heavy-chain antibody variable-region genes. Mol. Cell Biol. 10, 5187–5196 (1990).
Lanning, D. K. & Knight, K. L. Somatic hypermutation: mutations 3′ of rabbit VDJ H-chain genes. J. Immunol. 159, 4403–4407 (1997).
Parvari, R., Ziv, E., Lantner, F., Heller, D. & Schechter, I. Somatic diversification of chicken immunoglobulin light chains by point mutations. Proc. Natl Acad. Sci. USA 87, 3072–3076 (1990).
Gonzalez-Fernandez, A., Gupta, S. K., Pannell, R., Neuberger, M. S. & Milstein, C. Somatic mutation of immunoglobulin λ chains: a segment of the major intron hypermutates as much as the complementarity-determining regions. Proc. Natl Acad. Sci. USA 91, 12614–12618 (1994).
Weber, J. S., Berry, J., Manser, T. & Claflin, J. L. Mutations in Ig V(D)J genes are distributed asymmetrically and independently of the position of V(D)J. J. Immunol. 153, 3594–3602 (1994).
Rada, C., Gonzalez-Fernandez, A., Jarvis, J. M. & Milstein, C. The 5′ boundary of somatic hypermutation in a Vκ gene is in the leader intron. Eur. J. Immunol. 24, 1453–1457 (1994).
Gonzalez-Fernandez, A. & Milstein, C. Analysis of somatic hypermutation in mouse Peyer's patches using immunoglobulin κ light-chain transgenes. Proc. Natl Acad. Sci. USA 90, 9862–9866 (1993).
Storb, U. et al. A hypermutable insert in an immunoglobulin transgene contains hotspots of somatic mutation and sequences predicting highly stable structures in the RNA transcript. J. Exp. Med. 188, 689–698 (1998).
Hackett, J., Rogerson, B. J., O'Brien, R. L. & Storb, U. Analysis of somatic mutations in κ transgenes. J. Exp. Med. 172, 131–137 (1990).
Levy, Y. et al. Defect in IgV gene somatic hypermutation in common variable immuno-deficiency syndrome. Proc. Natl Acad. Sci. USA 95, 13135–13140 (1998).
Glazko, G. V., Milanesi, L. & Rogozin, I. B. The subclass approach for mutational spectrum analysis: application of the SEM algorithm. J. Theor. Biol. 192, 475–487 (1998).
Brenner, S. & Milstein, C. Origin of antibody variation. Nature 211, 242–243 (1966).
Kim, N. & Storb, U. The role of DNA repair in somatic hypermutation of immunoglobulin genes. J. Exp. Med. 187, 1729–1733 (1998).
Harris, R. S., Kong, Q. & Maizels, N. Somatic hypermutation and the three R's: repair, replication and recombination. Mutation Res. 436, 157–178 (1999).
Poltoratsky, V., Goodman, M. F. & Scharff, M. D. Error-prone candidates vie for somatic mutation. J. Exp. Med. 192, 27–30 (2000).
Goodman, M. F. & Tippin, B. The expanding polymerase universe. Nature Rev. Mol. Cell Biol. 1, 101–109 (2000).
Johnson, R. E., Washington, M. T., Prakash, S. & Prakash, L. Bridging the gap: a family of novel DNA polymerases that replicate faulty DNA. Proc. Natl Acad. Sci. USA 96, 12224–12226 (1999).
Friedberg, E. C., Feaver, W. J. & Gerlach, V. L. The many faces of DNA polymerases: strategies for mutagenesis and for mutational avoidance. Proc. Natl Acad. Sci. USA 97, 5681–5683 (2000).
Roberts, J. D. & Kunkel, T. A. in DNA Replication in Eukaryotic Cells: Concepts, enzymes and systems (ed. Pamphilis, M. D.) 217–247 (Cold Spring Harbor Laboratories, Cold Spring Harbor, New York, 1996).
Johnson, R. E., Kondratick, C. M., Prakash, S. & Prakash, L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285, 263–265 (1999).
Masutani, C. et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399, 700–704 (1999).
Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F. & Kunkel, T. A. Low fidelity DNA synthesis by human DNA polymerase-η. Nature 404, 1011–1013 (2000).
Bebenek, K., Matsuda, T., Masutani, C., Hanaoka, F. & Kunkel, T. A. Proofreading of DNA polymerase η-dependent replication errors. J. Biol. Chem. 276, 2317–2320 (2001).
Storb, U. et al. Somatic hypermutation of immunoglobulin genes is linked to transcription. Curr. Top. Microbiol. Immunol. 229, 11–19 (1998).
Spencer, J., Dunn, M. & Dunn-Walters, D. K. Characteristics of sequences around individual nucleotide substitutions in IgVH genes suggest different GC and AT mutators. J. Immunol. 162, 6596–6601 (1999).
Ohashi, E. et al. Fidelity and processivity of DNA synthesis by DNA polymerase κ, the product of the human DINB1 gene. J. Biol. Chem. 275, 39678–39684 (2000).
Kolchanov, N. A., Solovyov, V. V. & Rogozin, I. B. Peculiarities of immunoglobulin gene structures as a basis for somatic mutation emergence. FEBS Lett. 214, 87–91 (1987).
Golding, G. B., Gearhart, P. J. & Glickman, B. W. Patterns of somatic mutations in immunoglobulin variable genes. Genetics 115, 169–176 (1987).
Rogozin, I. B., Solovyov, V. V. & Kolchanov, N. A. Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection. Biochim. Biophys. Acta 1089, 175–182 (1991).
Zeng, X. et al. DNA polymerase η is an A-T mutator in somatic hypermutation of immunglobulin variable genes. Nature Immunol. 2, 537–541 (2001).
Kunkel, T. A. The mutational specificity of DNA polymerases-α and -γ during in vitro DNA synthesis. J. Biol. Chem. 260, 12866–12874 (1985).
Kunkel, T. A. The mutational specificity of DNA polymerase-β during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J. Biol. Chem. 260, 5787–5796 (1985).
Bebenek, K., Abbotts, J., Roberts, J. D., Wilson, S. H. & Kunkel, T. A. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J. Biol. Chem. 264, 16948–16956 (1989).
Rogozin, I. B., Kondrashev, F. A. & Glazko, G. V. Use of mutation spectra analysis software. Hum. Mutation 17, 83–102 (2001).
Oprea, M., Cowell, L.G. & Kepler, T.B. The targeting of somatic hypermutation closely resembles that of meiotic mutation. J. Immunol. 166, 892–899 (2001).
Acknowledgements
Partly supported by RFFR (grant No. 99-04-49535). We thank V. K. Nguyen, B. A. Rogozin, E. V. Koonin, J. Drake, A. Aksenova and W. C. Copeland for helpful discussion and comments on the manuscript.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Rogozin, I., Pavlov, Y., Bebenek, K. et al. Somatic mutation hotspots correlate with DNA polymerase η error spectrum. Nat Immunol 2, 530–536 (2001). https://doi.org/10.1038/88732
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/88732
This article is cited by
-
Diverse mutational landscapes in human lymphocytes
Nature (2022)
-
Unravelling roles of error-prone DNA polymerases in shaping cancer genomes
Oncogene (2021)
-
High-risk follicular lymphomas harbour more somatic mutations including those in the AID-motif
Scientific Reports (2017)
-
Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers
Scientific Reports (2016)
-
Hypermutation in human cancer genomes: footprints and mechanisms
Nature Reviews Cancer (2014)