Replication and Subnuclear Location Dynamics of the Immunoglobulin Heavy-Chain Locus in B-Lineage Cells

REFERENCES

• Alt, F., N. Rosenberg, S. Lewis, E. Thomas, and D. Baltimore. 1981. Organization and reorganization of immunoglobulin genes in A-MULV-transformed cells: rearrangement of heavy but not light chain genes. Cell 27: 381–390.
   PubMed Web of Science ®Google Scholar
• Alt, F. W., N. Rosenberg, V. Enea, E. Siden, and D. Baltimore. 1982. Multiple immunoglobulin heavy-chain gene transcripts in Abelson murine leukemia virus-transformed lymphoid cell lines. Mol. Cell. Biol. 2: 386–400.
   PubMed Web of Science ®Google Scholar
• Alwine, J. C. 1981. Hybridization analysis of specific RNAs by electrophoretic separation in agarose gels and transfer to diazobenzyloxymethyl paper. Gene Amplif. Anal. 2: 565–572.
   PubMedGoogle Scholar
• Angelin-Duclos, C., and K. Calame. 1998. Evidence that immunoglobulin VH-DJ recombination does not require germ line transcription of the recombining variable gene segment. Mol. Cell. Biol. 18: 6253–6264.
   PubMed Web of Science ®Google Scholar
• Ariizumi, K., Z. Wang, and P. W. Tucker. 1993. Immunoglobulin heavy chain enhancer is located near or in an initiation zone of chromosomal DNA replication. Proc. Natl. Acad. Sci. USA 90: 3695–3699.
   PubMedGoogle Scholar
• Berezney, R., D. D. Dubey, and J. A. Huberman. 2000. Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108: 471–484.
   PubMed Web of Science ®Google Scholar
• Boggs, B. A., and A. C. Chinault. 1997. Analysis of DNA replication by fluorescence in situ hybridization. Methods 13: 259–270.
   PubMedGoogle Scholar
• Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463–475.
   PubMed Web of Science ®Google Scholar
• Bridger, J. M., S. Boyle, I. R. Kill, and W. A. Bickmore. 2000. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr. Biol. 10: 149–152.
   PubMed Web of Science ®Google Scholar
• Brodeur, P. H., M. A. Thompson, and R. J. Riblet. 1984. The content and organization of mouse Igh-V families. UCLA Symp. Mol. Cell. Biol. 18: 445–453.
   Google Scholar
• Brown, E. H., M. A. Iqbal, S. Stuart, K. S. Hatton, J. Valinsky, and C. L. Schildkraut. 1987. Rate of replication of the murine immunoglobulin heavy-chain locus: evidence that the region is part of a single replicon. Mol. Cell. Biol. 7: 450–457.
   PubMedGoogle Scholar
• Caspi, Y., M. Taya, N. Hollander, and J. Haimovich. 1995. Light chain loss and reexpression leads to idiotype switch. Surrogate light chains are probably responsible for this process. Curr. Top. Microbiol. Immunol. 194: 179–186.
   PubMedGoogle Scholar
• Chevillard, C., J. Ozaki, C. Herring, and R. Riblet. 2002. A 3 megabase yeast artificial chromosome contig spanning the C57BL mouse Igh locus. J. Immunol. 168: 5659–5666.
   PubMedGoogle Scholar
• Cockell, M., and S. M. Gasser. 1999. Nuclear compartments and gene regulation. Curr. Opin. Genet. Dev. 9: 119–205.
   Google Scholar
• Cohn, M., G. Notani, and S. A. Rice. 1969. Characterization of the antibody to the C-carbohydrate produced by a transplantable mouse plasmacytoma. Immunochemistry 6: 111–123.
   PubMedGoogle Scholar
• Croft, J. A., J. M. Bridger, S. Boyle, P. Perry, P. Teague, and W. A. Bickmore. 1999. Differences in the localization and morphology of chromosomes in the human nucleus. J. Cell Biol. 145: 1119–1131.
   PubMed Web of Science ®Google Scholar
• Csink, A. K., and S. Henikoff. 1998. Large-scale chromosomal movements during interphase progression in Drosophila. J. Cell Biol. 143: 13–22.
   PubMedGoogle Scholar
• Dalgaard, J. Z., and A. J. Klar. 1999. Orientation of DNA replication establishes mating-type switching pattern in S. pombe. Nature 400: 181–184.
   PubMed Web of Science ®Google Scholar
• Dalgaard, J. Z., and A. J. Klar. 2001. Does S. pombe exploit the intrinsic asymmetry of DNA synthesis to imprint daughter cells for mating-type switching? Trends Genet. 17: 153–157.
   PubMedGoogle Scholar
• DePamphilis, M. L. 1999. Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21: 5–16.
   PubMedGoogle Scholar
• DePamphilis, M. L. 2000. Review: nuclear structure and DNA replication. J. Struct. Biol. 129: 186–197.
   PubMed Web of Science ®Google Scholar
• Dijkwel, P. A., and J. L. Hamlin. 1999. Physical and genetic mapping of mammalian replication origins. Methods 18: 418–431.
   PubMedGoogle Scholar
• Dutta, A., and S. P. Bell. 1997. Initiation of DNA replication in eukaryotic cells. Annu. Rev. Cell Dev. Biol. 13: 293–332.
   PubMed Web of Science ®Google Scholar
• Edenberg, H. J., and J. A. Huberman. 1975. Eukaryotic chromosome replication. Annu. Rev. Genet. 9: 245–284.
   PubMed Web of Science ®Google Scholar
• Ermakova, O. V., L. Nguyen, R. D. Little, N. Ashouian, R. Riblet, B. K. Birshtein, and C. L. Schildkraut. 1999. Evidence that a single replication fork proceeds from early to late replicating domains in the Igh locus in a non B cell line. Mol. Cell 3: 321–330.
   PubMedGoogle Scholar
• Friedman, K. L., and B. J. Brewer. 1995. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Methods Enzymol. 262: 613–627.
   PubMed Web of Science ®Google Scholar
• Friedman, K. L., J. D. Diller, B. M. Ferguson, S. V. Nyland, B. J. Brewer, and W. L. Fangman. 1996. Multiple determinants controlling activation of yeast replication origins late in S phase. Genes Dev. 10: 1595–1607.
   PubMedGoogle Scholar
• Gilbert, D. M. 2001. Nuclear position leaves its mark on replication timing. J. Cell Biol. 152: F11–F16.
   PubMedGoogle Scholar
• Gillies, S. D., S. L. Morrison, V. T. Oi, and S. Tonegawa. 1983. A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell 33: 717–728.
   PubMed Web of Science ®Google Scholar
• Gregor, P. D., and S. L. Morrison. 1986. Myeloma mutant with a novel 3′ flanking region: loss of normal sequence and insertion of repetitive elements leads to decreased transcription but normal processing of the alpha heavy-chain gene products. Mol. Biol. Cell 6: 1903–1916.
   Google Scholar
• Haber, J. E. 2001. Hypermutation: give us a break. Nat. Immunol. 2: 902–903.
   PubMedGoogle Scholar
• Haines, B. B., and P. H. Brodeur. 1998. Accessibility changes across the mouse Igh-V locus during B cell development. Eur. J. Immunol. 28: 4228–4235.
   PubMedGoogle Scholar
• Hartman, A. B., and S. Rudikoff. 1984. VH genes encoding the immune response to beta-(1,6)-galactan: somatic mutation in IgM molecules. EMBO J. 3: 3023–3030.
   PubMed Web of Science ®Google Scholar
• Hatton, K. S., V. Dhar, E. H. Brown, M. A. Iqbal, S. Stuart, V. T. Didamo, and C. L. Schildkraut. 1988. Replication program of active and inactive multigene families in mammalian cells. Mol. Cell. Biol. 8: 2149–2158.
   PubMed Web of Science ®Google Scholar
• Hatton, K. S., V. Dhar, T. A. Gahn, E. H. Brown, D. Mager, and C. L. Schildkraut. 1988. Temporal order of replication of multigene families reflects chromosomal location and transcriptional activity. Cancer Cells 6: 335–340.
   Google Scholar
• Hatton, K. S., and C. L. Schildkraut. 1990. The mouse immunoglobulin kappa light chain genes are located in early and late replicating regions of chromosome 6. Mol. Cell. Biol. 10: 4314–4323.
   PubMedGoogle Scholar
• Heun, P., T. Laroche, M. K. Raghuraman, and S. M. Gasser. 2001. The positioning and dynamics of origins of replication in the budding yeast nucleus. J. Cell Biol. 152: 385–400.
   PubMed Web of Science ®Google Scholar
• Jackson, D. A., and A. Pombo. 1998. Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J. Cell Biol. 140: 1285–1295.
   PubMed Web of Science ®Google Scholar
• Kirsch, I. R., J. V. Ravetch, S. P. Kwan, E. E. Max, R. L. Ney, and P. Leder. 1981. Multiple immunoglobulin switch region homologies outside the heavy chain constant region locus. Nature 293: 585–587.
   PubMed Web of Science ®Google Scholar
• Kosak, S. T., J. Skok, M. M. Le Beau, R. Riblet, A. G. Fisher, and H. Singh. 2002. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296: 158–162.
   PubMed Web of Science ®Google Scholar
• Li, F., J. Chen, M. Izumi, M. C. Butler, S. M. Keezer, and D. M. Gilbert. 2001. The replication timing program of the Chinese hamster beta-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase. J. Cell Biol. 154: 283–292.
   PubMedGoogle Scholar
• Maes, J., Y. Caspi, F. Rougeon, J. Haimovich, and M. Goodhardt. 2000. Secondary V(D)J rearrangements and B cell receptor-mediated down-regulation of recombination activating gene-2 expression in a murine B cell line. J. Immunol. 165:703–709.
   PubMedGoogle Scholar
• Maes, J., L. P. O'Neill, P. Cavelier, B. M. Turner, F. Rougeon, and M. Goodhardt. 2001. Chromatin remodeling at the Ig loci prior to V(D)J recombination. J. Immunol. 167: 866–874.
   PubMedGoogle Scholar
• Mainville, C. A., K. M. Sheehan, L. D. Klaman, C. A. Giorgetti, J. L. Press, and P. H. Brodeur. 1996. Deletional mapping of fifteen mouse VH gene families reveals a common organization for three Igh haplotypes. J. Immunol. 156: 1038–1046.
   PubMedGoogle Scholar
• Max, E. E. 1999. Immunoglobulins: molecular genetics, p. 111–182. In W. E. Paul (ed.), Fundamental immunology, 4th ed. Lippincott-Raven Press, New York, N.Y.
   Google Scholar
• McMurry, M. T., and M. S. Krangel. 2000. A role for histone acetylation in the developmental regulation of VDJ recombination. Science 287: 495–498.
   PubMed Web of Science ®Google Scholar
• Michaelson, J. S., O. Ermakova, B. K. Birshtein, N. Ashouian, C. Chevillard, R. Riblet, and C. L. Schildkraut. 1997. Regulation of the replication of the murine immunoglobulin heavy chain gene locus: evaluation of the role of the 3′ regulatory region. Mol. Cell. Biol. 17: 6167–6174.
   PubMedGoogle Scholar
• Mostoslavsky, R., N. Singh, T. Tenzen, M. Goldmit, C. Gabay, S. Elizur, P. Qi, B. E. Reubinoff, A. Chess, H. Cedar, and Y. Bergman. 2001. Asynchronous replication and allelic exclusion in the immune system. Nature 414: 221–225.
   PubMed Web of Science ®Google Scholar
• Nakayasu, H., and R. Berezney. 1989. Mapping replicational sites in the eucaryotic cell nucleus. J. Cell Biol. 108: 1–11.
   PubMed Web of Science ®Google Scholar
• Nawotka, K. A., and J. A. Huberman. 1988. Two-dimensional gel electrophoretic method for mapping DNA replicons. Mol. Cell. Biol. 8: 1408–1413.
   PubMedGoogle Scholar
• Nelson, K. J., J. Haimovich, and R. P. Perry. 1983. Characterization of productive and sterile transcripts from the immunoglobulin heavy-chain locus: processing of μm and μs mRNA. Mol. Cell. Biol. 3: 1317–1332.
   PubMedGoogle Scholar
• Pennell, C. A., K. M. Sheehan, P. H. Brodeur, and S. H. Clarke. 1989. Organization and expression of VH gene families preferentially expressed by Ly-1+ (CD5) B cells. Eur. J. Immunol. 19: 2115–2121.
   PubMedGoogle Scholar
• Saleque, S., M. Singh, and B. K. Birshtein. 1999. Ig heavy chain expression and class switching in vitro from an allele lacking the 3′ enhancers DNase I-hypersensitive hs3A and hs1,2. J. Immunol. 162: 2791–2803.
   PubMedGoogle Scholar
• Saleque, S., M. Singh, R. D. Little, S. L. Giannini, J. S. Michaelson, and B. K. Birshtein. 1997. Dyad symmetry within the mouse 3′ IgH regulatory region includes two virtually identical enhancers (C alpha3′E and hs3). J. Immunol. 158: 4780–4787.
   PubMedGoogle Scholar
• Selig, S., K. Okumura, D. C. Ward, and H. Cedar. 1992. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J. 11: 1217–1225.
   PubMed Web of Science ®Google Scholar
• Sharma, K., M. Weinberger, and J. A. Huberman. 2001. Roles for internal and flanking sequences in regulating the activity of mating-type-silencer associated replication origins in Saccharomyces cerevisiae. Genetics 159: 35–45.
   PubMedGoogle Scholar
• Shimizu, A., N. Takahashi, Y. Yaoita, and T. Honjo. 1982. Organization of the constant-region gene family of the mouse immunoglobulin heavy chain. Cell 28: 499–506.
   PubMed Web of Science ®Google Scholar
• Simon, I., and H. Cedar. 1996. Temporal order of DNA replication, p. 387–408. In M. L. DePamphilis (ed.), DNA replication in eukaryotic cells. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Simon, I., T. Tenzen, B. E. Reubinoff, D. Hillman, J. R. McCarrey, and H. Cedar. 1999. Asynchronous replication of imprinted genes is established in the gametes and maintained during development. Nature 401: 929–932.
   PubMed Web of Science ®Google Scholar
• Skok, J. A., K. E. Brown, V. Azuara, M. L. Caparros, J. Baxter, K. Takacs, N. Dillon, D. Gray, R. P. Perry, M. Merkenschlager, and A. G. Fisher. 2001. Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat. Immunol. 2: 848–854.
   PubMed Web of Science ®Google Scholar
• Wahl, M. R., G. B. Beck-Engeser, and P. D. Burrows. 1984. Allelic inclusion in the pre-B-cell line 18-81. Proc. Natl. Acad. Sci. USA 81: 867–870.
   PubMedGoogle Scholar
• Wang, X. F., and K. Calame. 1985. The endogenous immunoglobulin heavy chain enhancer can activate tandem VH promoters separated by a large distance. Cell 43: 659–665.
   PubMed Web of Science ®Google Scholar
• Yancopoulos, G. D., and F. W. Alt. 1985. Developmentally controlled and tissue-specific expression of unrearranged VH gene segments. Cell 40: 271–281.
   PubMed Web of Science ®Google Scholar