The influence of transcriptional orientation on endogenous switch region function (original) (raw)

References

  1. Manis, J.P., Tian, M. & Alt, F.W. Mechanism and control of class-switch recombination. Trends Immunol. 23, 31–39 (2002).
    Article CAS PubMed Google Scholar
  2. Honjo, T., Kinoshita, K. & Muramatsu, M. Molecular mechanism of class switch recombination: linkage with somatic hypermutation. Annu. Rev. Immunol. 20, 165–196 (2002).
    Article CAS PubMed Google Scholar
  3. Dunnick, W., Hertz, G.Z., Scappino, L. & Gritzmacher, C. DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res. 21, 365–372 (1993).
    Article CAS PubMed PubMed Central Google Scholar
  4. Lee, C.G., Kondo, S. & Honjo, T. Frequent but biased class switch recombination in the Sμ flanking regions. Curr. Biol. 8, 227–230 (1998).
    Article CAS PubMed Google Scholar
  5. Shanmugam, A., Shi, M.J., Yauch, L., Stavnezer, J. & Kenter, A.L. Evidence for class-specific factors in immunoglobulin isotype switching. J. Exp. Med. 191, 1365–1380 (2000).
    Article CAS PubMed PubMed Central Google Scholar
  6. Ma, L., Wortis, H.H. & Kenter, A.L. Two new isotype-specific switching activities detected for Ig class switching. J. Immunol. 168, 2835–2846 (2002).
    Article CAS PubMed Google Scholar
  7. Reaban, M.E. & Griffin, J.A. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature 348, 342–344 (1990).
    Article CAS PubMed Google Scholar
  8. Reaban, M.E., Lebowitz, J. & Griffin, J.A. Transcription induces the formation of a stable RNA-DNA hybrid in the immunoglobulin α switch region. J. Biol. Chem. 269, 21850–21857 (1994).
    CAS PubMed Google Scholar
  9. Daniels, G.A. & Lieber, M.R. RNA:DNA complex formation upon transcription of immunoglobulin switch regions: implications for the mechanism and regulation of class switch recombination. Nucleic Acids Res. 23, 5006–5011 (1995).
    Article CAS PubMed PubMed Central Google Scholar
  10. Dempsey, L.A., Sun, H., Hanakahi, L.A. & Maizels, N. G4 DNA binding by LR1 and its subunits, nucleolin and hnRNP D, A role for G-G pairing in immunoglobulin switch recombination. J. Biol. Chem. 274, 1066–1071 (1999).
    Article CAS PubMed Google Scholar
  11. Tian, M. & Alt, F.W. Transcription-induced cleavage of immunoglobulin switch regions by nucleotide excision repair nucleases in vitro. J. Biol. Chem. 275, 24163–24172 (2000).
    Article CAS PubMed Google Scholar
  12. Mizuta, R. et al. Molecular visualization of immunoglobulin switch region RNA/DNA complex by atomic force microscope. J. Biol. Chem. 278, 4431–4434 (2003).
    Article CAS PubMed Google Scholar
  13. Mussmann, R., Courtet, M., Schwager, J. & Du Pasquier, L. Microsites for immunoglobulin switch recombination breakpoints from Xenopus to mammals. Eur. J. Immunol. 27, 2610–2619 (1997).
    Article CAS PubMed Google Scholar
  14. Tashiro, J., Kinoshita, K. & Honjo, T. Palindromic but not G-rich sequences are targets of class switch recombination. Int. Immunol. 13, 495–505 (2001).
    Article CAS PubMed Google Scholar
  15. Luby, T.M., Schrader, C.E., Stavnezer, J. & Selsing, E. The μ switch region tandem repeats are important, but not required, for antibody class switch recombination. J. Exp. Med. 193, 159–168 (2001).
    Article CAS PubMed PubMed Central Google Scholar
  16. Lutzker, S., Rothman, P., Pollock, R., Coffman, R. & Alt, F.W. Mitogen- and IL-4-regulated expression of germ-line Igγ2b transcripts: evidence for directed heavy chain class switching. Cell 53, 177–184 (1988).
    Article CAS PubMed Google Scholar
  17. Berton, M.T., Uhr, J.W. & Vitetta, E.S. Synthesis of germ-line γ1 immunoglobulin heavy-chain transcripts in resting B cells: induction by interleukin 4 and inhibition by interferon γ. Proc. Natl. Acad. Sci. USA 86, 2829–2833 (1989).
    Article CAS PubMed PubMed Central Google Scholar
  18. Xu, M. & Stavnezer, J. Structure of germline immunoglobulin heavy-chain γ1 transcripts in interleukin 4 treated mouse spleen cells. Dev. Immunol. 1, 11–17 (1990).
    Article CAS PubMed PubMed Central Google Scholar
  19. Rothman, P. et al. Structure and expression of germline immunoglobulin γ3 heavy chain gene transcripts: implications for mitogen and lymphokine directed class-switching. Int. Immunol. 2, 621–627 (1990).
    Article CAS PubMed Google Scholar
  20. Rothman, P. et al. Structure and expression of germ line immunoglobulin heavy-chain ε transcripts: interleukin-4 plus lipopolysaccharide-directed switching to Cε . Mol. Cell. Biol. 10, 1672–1679 (1990).
    Article CAS PubMed PubMed Central Google Scholar
  21. Collins, J.T. & Dunnick, W.A. Germline transcripts of the murine immunoglobulin γ2a gene: structure and induction by IFN-γ. Int. Immunol. 5, 885–891 (1993).
    Article CAS PubMed Google Scholar
  22. Jung, S., Rajewsky, K. & Radbruch, A. Shutdown of class switch recombination by deletion of a switch region control element. Science 259, 984–987 (1993).
    Article CAS PubMed Google Scholar
  23. Zhang, J., Bottaro, A., Li, S., Stewart, V. & Alt, F.W. A selective defect in IgG2b switching as a result of targeted mutation of the Iγ2b promoter and exon. EMBO J. 12, 3529–3537 (1993).
    Article CAS PubMed PubMed Central Google Scholar
  24. Bottaro, A. et al. S region transcription per se promotes basal IgE class switch recombination but additional factors regulate the efficiency of the process. EMBO J. 13, 665–674 (1994).
    Article CAS PubMed PubMed Central Google Scholar
  25. Lorenz, M., Jung, S. & Radbruch, A. Switch transcripts in immunoglobulin class switching. Science 267, 1825–1828 (1995).
    Article CAS PubMed Google Scholar
  26. Harriman, G.R., Bradley, A., Das, S., Rogers-Fani, P. & Davis, A.C. IgA class switch in Iα exon-deficient mice. Role of germline transcription in class switch recombination. J. Clin. Invest. 97, 477–485 (1996).
    Article CAS PubMed PubMed Central Google Scholar
  27. Seidl, K.J. et al. An expressed _neo_r cassette provides required functions of the Iγ2b exon for class switching. Int. Immunol. 10, 1683–1692 (1998).
    Article CAS PubMed Google Scholar
  28. Daniels, G.A. & Lieber, M.R. Strand specificity in the transcriptional targeting of recombination at immunoglobulin switch sequences. Proc. Natl. Acad. Sci. USA. 92, 5625–5629 (1995).
    Article CAS PubMed PubMed Central Google Scholar
  29. Kinoshita, K., Tashiro, J., Tomita, S., Lee, C.G. & Honjo, T. Target specificity of immunoglobulin class switch recombination is not determined by nucleotide sequences of S regions. Immunity 9, 849–858 (1998).
    Article CAS PubMed Google Scholar
  30. von Schwedler, U., Jack, H.M. & Wabl, M. Beswitched. The looping out model for immunoglobulin class switching. New Biol. 8, 657–662 (1990).
    Google Scholar
  31. Muramatsu, M. et al. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J. Biol. Chem. 274, 18470–18476 (1999).
    Article CAS PubMed Google Scholar
  32. 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 PubMed Google Scholar
  33. Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102, 565–575 (2000).
    Article CAS PubMed Google Scholar
  34. Petersen, S. et al. AID is required to initiate Nbs1/γ-H2AX. Nature 414, 660–665 (2001).
    Article CAS PubMed PubMed Central Google Scholar
  35. Petersen-Mahrt, S.K., Harris, R.S. & Neuberger, M.S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418, 99–103 (2002).
    Article CAS PubMed Google Scholar
  36. Weill, J.C. et al. Ig gene hypermutation: a mechanism is due. Adv. Immunol. 80, 183–202 (2002).
    Article CAS PubMed Google Scholar
  37. Papavasiliou, F.N. & Schatz, D.G. Somatic hypermutation of immunoglobulin genes: merging mechanisms for genetic diversity. Cell 109 (Suppl.), S35–S44 (2002).
    Article CAS PubMed Google Scholar
  38. Chester, A., Scott, J., Anant, S. & Navaratnam, N. RNA editing: cytidine to uridine conversion in apolipoprotein B mRNA. Biochim. Biophys. Acta. 1494, 1–13 (2000).
    Article CAS PubMed Google Scholar
  39. Di Noia, J. & Neuberger, M.S. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase. Nature 419, 43–48 (2002).
    Article CAS PubMed Google Scholar
  40. Rada, C. et al. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr. Biol. 12, 1748–1755 (2002).
    Article CAS PubMed Google Scholar
  41. Stavnezer, J. & Bradley, S.P. Does activation-induced deaminase initiate antibody diversification by DNA deamination? Trends Genet. 18, 541–543 (2002).
    Article CAS PubMed Google Scholar
  42. Storb, U. & Stavnezer, J. Immunoglobulin genes: generating diversity with AID and UNG. Curr Biol. 12, R725–R727 (2002).
    Article CAS PubMed Google Scholar
  43. Dudley, D.D. et al. Internal IgH class switch region deletions are position-independent and enhanced by AID expression. Proc. Natl. Acad. Sci. USA 99, 9984–9989 (2002).
    Article CAS PubMed PubMed Central Google Scholar
  44. Nagaoka, H., Muramatsu, M., Yamamura, N., Kinoshita, K. & Honjo, T. Activation-induced deaminase (AID)-directed hypermutation in the immunoglobulin Sμ region: implication of AID involvement in a common step of class switch recombination and somatic hypermutation. J. Exp. Med. 195, 529–534 (2002).
    Article CAS PubMed PubMed Central Google Scholar
  45. Yancopoulos, G.D. et al. Secondary genomic rearrangement events in pre-B cells: VHDJH replacement by a LINE-1 sequence and directed class switching. EMBO J. 5, 3259–3266 (1986).
    Article CAS PubMed PubMed Central Google Scholar
  46. Stavnezer, J. et al. Immunoglobulin heavy-chain switching may be directed by prior induction of transcripts from constant-region genes. Proc. Natl. Acad. Sci. USA 85, 7704–7708 (1988).
    Article CAS PubMed PubMed Central Google Scholar
  47. Sakai, E., Bottaro, A., Davidson, L., Sleckman, B.P. & Alt, F.W. Recombination and transcription of the endogenous Ig heavy chain locus is effected by the Ig heavy chain intronic enhancer core region in the absence of the matrix attachment regions. Proc. Natl. Acad. Sci. USA 96, 1526–1531 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  48. Sleckman, B.P., Khor, B., Monroe, R. & Alt, F.W. Assembly of productive T cell receptor δ variable region genes exhibits allelic inclusion. J. Exp. Med. 188, 1465–1471 (1998).
    Article CAS PubMed PubMed Central Google Scholar
  49. Chen, J., Lansford, R., Stewart, V., Young, F. & Alt, F.W. RAG-2-deficient blastocyst complementation: an assay of gene function in lymphocyte development. Proc. Natl. Acad. Sci. USA 90, 4528–4532 (1993).
    Article CAS PubMed PubMed Central Google Scholar
  50. Hein, K. et al. Processing of switch transcripts is required for targeting of antibody class switch recombination. J. Exp. Med. 188, 2369–2374 (1998).
    Article CAS PubMed PubMed Central Google Scholar
  51. Radbruch, A., Muller, W. & Rajewsky, K. Class switch recombination is IgG1 specific on active and inactive IgH loci of IgG1-secreting B-cell blasts. Proc. Natl. Acad. Sci. USA 83, 3954–3957 (1986).
    Article CAS PubMed PubMed Central Google Scholar
  52. Hummel, M., Berry, J.K. & Dunnick, W. Switch region content of hybridomas: the two spleen cell Igh loci tend to rearrange to the same isotype. J. Immunol. 138, 3539–3548 (1987).
    CAS PubMed Google Scholar
  53. Winter, E., Krawinkel, U. & Radbruch, A. Directed Ig class switch recombination in activated murine B cells. EMBO J. 6, 1663–1671 (1987).
    Article CAS PubMed PubMed Central Google Scholar
  54. Schultz, C. et al. Patterns and extent of isotype-specificity in the murine H chain switch DNA rearrangement. J. Immunol. 144, 363–370 (1990).
    CAS PubMed Google Scholar
  55. Jung, S., Siebenkotten, G. & Radbruch, A. Frequency of immunoglobulin E class switching is autonomously determined and independent of prior switching to other classes. J. Exp. Med. 179, 2023–2026 (1994).
    Article CAS PubMed Google Scholar
  56. Ratmeyer, L., Vinayak, R., Zhong, Y.Y., Zon, G. & Wilson, W.D. Sequence specific thermodynamic and structural properties for DNA-RNA duplexes. Biochemistry 33, 5298–5304 (1994).
    Article CAS PubMed Google Scholar
  57. Yu, K., Chedin, F., Hsieh, C.-L., Wilson, T.E. & Lieber, M.R. R-loops at immunoglobulin class switch regions within the chromosomes of stimulated B cells. Nature Immunology, advance online publication, 7 april 2003 (doi:10.1038/ni919).
  58. Chaudhuri, J., Tian, M., Khuong, C., Chua, K., Pinaud, E. & Alt, F.W. Transcription targeted DNA deamination by the AID antibody diversification enzyme. Nature, in press.

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