Two levels of protection for the B cell genome during somatic hypermutation (original) (raw)

• Di Noia, J. M. & Neuberger, M. S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76, 1–22 (2007)
  Article CAS Google Scholar
• Kuppers, R. & Dalla-Favera, R. Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene 20, 5580–5594 (2001)
  Article CAS Google Scholar
• Shen, H. M., Peters, A., Baron, B., Zhu, X. & Storb, U. Mutation of BCL-6 gene in normal B cells by the process of somatic hypermutation of Ig genes. Science 280, 1750–1752 (1998)
  Article CAS ADS Google Scholar
• Pasqualucci, L. et al. BCL-6 mutations in normal germinal center B cells: evidence of somatic hypermutation acting outside Ig loci. Proc. Natl Acad. Sci. USA 95, 11816–11821 (1998)
  Article CAS ADS Google Scholar
• Gordon, M. S., Kanegai, C. M., Doerr, J. R. & Wall, R. Somatic hypermutation of the B cell receptor genes B29 (Ig beta, CD79b) and mb1 (Ig alpha, CD79a). Proc. Natl Acad. Sci. USA 100, 4126–4131 (2003)
  Article CAS ADS Google Scholar
• Muschen, M. et al. Somatic mutation of the CD95 gene in human B cells as a side-effect of the germinal center reaction. J. Exp. Med. 192, 1833–1839 (2000)
  Article CAS Google Scholar
• Pasqualucci, L. et al. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature 412, 341–346 (2001)
  Article CAS ADS Google Scholar
• Parsa, J. Y. et al. AID mutates a non-immunoglobulin transgene independent of chromosomal position. Mol. Immunol. 44, 567–575 (2007)
  Article CAS Google Scholar
• Wang, C. L., Harper, R. A. & Wabl, M. Genome-wide somatic hypermutation. Proc. Natl Acad. Sci. USA 101, 7352–7356 (2004)
  Article CAS ADS Google Scholar
• Longerich, S., Basu, U., Alt, F. & Storb, U. AID in somatic hypermutation and class switch recombination. Curr. Opin. Immunol. 18, 164–174 (2006)
  Article CAS Google Scholar
• Fagarasan, S. et al. Critical roles of activation-induced cytidine deaminase in the homeostasis of gut flora. Science 298, 1424–1427 (2002)
  Article CAS ADS Google Scholar
• Shen, H. M., Michael, N., Kim, N. & Storb, U. The TATA binding protein, c-Myc and survivin genes are not somatically hypermutated, while Ig and BCL6 genes are hypermutated in human memory B cells. Int. Immunol. 12, 1085–1093 (2000)
  Article CAS Google Scholar
• Rada, C., Di Noia, J. M. & Neuberger, M. S. Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation. Mol. Cell 16, 163–171 (2004)
  Article CAS Google Scholar
• Shen, H. M., Tanaka, A., Bozek, G., Nicolae, D. & Storb, U. Somatic hypermutation and class switch recombination in _Msh6_-/-_Ung_-/- double-knockout mice. J. Immunol. 177, 5386–5392 (2006)
  Article CAS Google Scholar
• Xue, K., Rada, C. & Neuberger, M. S. The in vivo pattern of AID targeting to immunoglobulin switch regions deduced from mutation spectra in _msh2_-/-_ung_-/- mice. J. Exp. Med. 203, 2085–2094 (2006)
  Article CAS Google Scholar
• Michael, N. et al. The E box motif CAGGTG enhances somatic hypermutation without enhancing transcription. Immunity 19, 235–242 (2003)
  Article CAS Google Scholar
• Odegard, V. H. & Schatz, D. G. Targeting of somatic hypermutation. Nature Rev. Immunol. 6, 573–583 (2006)
  Article CAS Google Scholar
• Duquette, M. L., Huber, M. D. & Maizels, N. G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas. Cancer Res. 67, 2586–2594 (2007)
  Article CAS Google Scholar
• Franco, S. et al. H2AX prevents DNA breaks from progressing to chromosome breaks and translocations. Mol. Cell 21, 201–214 (2006)
  Article CAS Google Scholar
• Ramiro, A. R. et al. Role of genomic instability and p53 in AID-induced c-myc-Igh translocations. Nature 440, 105–109 (2006)
  Article CAS ADS Google Scholar
• Mullighan, C. G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758–764 (2007)
  Article CAS ADS Google Scholar
• Janz, S. Myc translocations in B cell and plasma cell neoplasms. DNA Repair (Amst.) 5, 1213–1224 (2006)
  Article CAS Google Scholar
• Poltoratsky, V., Prasad, R., Horton, J. K. & Wilson, S. H. Down-regulation of DNA polymerase beta accompanies somatic hypermutation in human BL2 cell lines. DNA Repair (Amst.) 6, 244–253 (2007)
  Article CAS Google Scholar
• Reynaud, C. A., Aoufouchi, S., Faili, A. & Weill, J. C. What role for AID: mutator, or assembler of the immunoglobulin mutasome? Nature Immunol. 4, 631–638 (2003)
  Article CAS Google Scholar
• Bindra, R. S. & Glazer, P. M. Co-repression of mismatch repair gene expression by hypoxia in cancer cells: Role of the Myc/Max network. Cancer Lett. 252, 93–103 (2007)
  Article CAS Google Scholar
• Rosenberg, B. R. & Papavasiliou, F. N. Beyond SHM and CSR: AID and related cytidine deaminases in the host response to viral infection. Adv. Immunol. 94, 215–244 (2007)
  Article CAS Google Scholar
• Epeldegui, M., Hung, Y. P., McQuay, A., Ambinder, R. F. & Martinez-Maza, O. Infection of human B cells with Epstein-Barr virus results in the expression of somatic hypermutation-inducing molecules and in the accrual of oncogene mutations. Mol. Immunol. 44, 934–942 (2007)
  Article CAS Google Scholar
• Machida, K. et al. Hepatitis C virus induces a mutator phenotype: enhanced mutations of immunoglobulin and protooncogenes. Proc. Natl Acad. Sci. USA 101, 4262–4267 (2004)
  Article CAS ADS Google Scholar
• Matsumoto, Y. et al. Helicobacter pylori infection triggers aberrant expression of activation-induced cytidine deaminase in gastric epithelium. Nature Med. 13, 470–476 (2007)
  Article CAS Google Scholar
• Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003)
  Article MathSciNet CAS ADS Google Scholar
• 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)
  Article CAS Google Scholar
• Reitmair, A. H. et al. MSH2 deficient mice are viable and susceptible to lymphoid tumours. Nature Genet. 11, 64–70 (1995)
  Article CAS Google Scholar
• Nilsen, H. et al. Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication. Mol. Cell 5, 1059–1065 (2000)
  Article CAS Google Scholar
• Yu, D. et al. Axon growth and guidance genes identify T-dependent germinal centre B cells. Immunol. Cell Biol. 86, 3–14 (2008)
  Article CAS Google Scholar
• Klein, U. et al. Transcriptional analysis of the B cell germinal center reaction. Proc. Natl Acad. Sci. USA 100, 2639–2644 (2003)
  Article CAS ADS Google Scholar
• Alizadeh, A. et al. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb. Symp. Quant. Biol. 64, 71–78 (1999)
  Article CAS Google Scholar
• Suzuki, Y., Yamashita, R., Nakai, K. & Sugano, S. DBTSS: DataBase of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30, 328–331 (2002)
  Article CAS Google Scholar
• Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177–183 (2004)
  Article CAS Google Scholar
• Auer, R. L. et al. Identification of a potential role for POU2AF1 and BTG4 in the deletion of 11q23 in chronic lymphocytic leukemia. Genes Chromosom. Cancer 43, 1–10 (2005)
  Article CAS Google Scholar
• Neuberger, M. S. et al. Monitoring and interpreting the intrinsic features of somatic hypermutation. Immunol. Rev. 162, 107–116 (1998)
  Article CAS Google Scholar
• Huang, X. On global sequence alignment. Comput. Appl. Biosci. 10, 227–235 (1994)
  CAS PubMed Google Scholar
• Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000)
  Article CAS ADS Google Scholar
• Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194 (1998)
  Article CAS Google Scholar
• Ewing, B., Hillier, L., Wendl, M. C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998)
  Article CAS Google Scholar
• Goossens, T., Klein, U. & Kuppers, R. Frequent occurrence of deletions and duplications during somatic hypermutation: implications for oncogene translocations and heavy chain disease. Proc. Natl Acad. Sci. USA 95, 2463–2468 (1998)
  Article CAS ADS Google Scholar
• Karolchik, D. et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32, D493–D496 (2004)
  Article CAS Google Scholar
• Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002)
  Article CAS Google Scholar
• Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005)
  Article CAS ADS Google Scholar