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Two levels of protection for the B cell genome during somatic hypermutation

Nature volume 451, pages 841–845 (2008)Cite this article

Abstract

Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by cytosine deamination by the activation-induced deaminase (AID) and completed by error-prone processing of the resulting uracils by mismatch and base excision repair factors1. Somatic hypermutation represents a threat to genome integrity2 and it is not known how the B cell genome is protected from the mutagenic effects of somatic hypermutation nor how often these protective mechanisms fail. Here we show, by extensive sequencing of murine B cell genes, that the genome is protected by two distinct mechanisms: selective targeting of AID and gene-specific, high-fidelity repair of AID-generated uracils. Numerous genes linked to B cell tumorigenesis, including Myc, Pim1, Pax5, Ocab (also called Pou2af1), H2afx, Rhoh and Ebf1, are deaminated by AID but escape acquisition of most mutations through the combined action of mismatch and base excision repair. However, approximately 25% of expressed genes analysed were not fully protected by either mechanism and accumulated mutations in germinal centre B cells. Our results demonstrate that AID acts broadly on the genome, with the ultimate distribution of mutations determined by a balance between high-fidelity and error-prone DNA repair.

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Figure 1: Gene mutation frequencies in wild-type and Aid -/- B cells.
Figure 2: Mutation frequencies in Msh2 -/- Ung -/- double knockout B cells.
Figure 3: Mutation frequencies in Msh2-deficient or Ung-deficient B cells.

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Acknowledgements

We thank C. Rada and M. Neuberger for providing initial samples of DNA from double knockout mice and for comments on the manuscript; L. Staudt, M. Tomayko and M. Shlomchik for unpublished microarray data; S. Fugmann for comments on the manuscript; S. Unniraman for numerous ideas and comments; and D. Tuck for advice on the bioinformatic analysis. We acknowledge the contributions of the Broad Sequencing Platform. This work was supported by a fellowship from the Anna Fuller Foundation (M.L.) and by the Howard Hughes Medical Institute.

Author Contributions M.L. and D.G.S. designed the experiments and M.L. generated all of the sequencing and expression data. M.L., J.L.D. and S.H.K. performed data and statistical analyses and created the figures. D.J.R., J.L.D. and S.H.K. wrote software for sequence analyses. C.G.V. and C.C.G. provided microarray expression data. D.G.S. wrote the paper. All authors commented on the manuscript.

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Author notes

  1. Daniel J. Richter

    Present address: Present address: Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, USA.,

Authors and Affiliations

  1. Department of Immunobiology,,

    Man Liu & David G. Schatz

  2. Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA,

    Steven H. Kleinstein

  3. Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA,

    Jamie L. Duke & Steven H. Kleinstein

  4. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02141, USA ,

    Daniel J. Richter

  5. Division of Immunology and Genetics, John Curtin School of Medical Research, The Australian National University,

    Carola G. Vinuesa & Christopher C. Goodnow

  6. Australian Phenomics Facility, Canberra, ACT 2601, Australia ,

    Christopher C. Goodnow

  7. Howard Hughes Medical Institute, New Haven, Connecticut 06510, USA ,

    David G. Schatz

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Correspondence to David G. Schatz.

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Liu, M., Duke, J., Richter, D. et al. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841–845 (2008). https://doi.org/10.1038/nature06547

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