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. 1992 Dec;11(13):4869–4875. doi: 10.1002/j.1460-2075.1992.tb05593.x

Biased reading frames of pre-existing DH--JH coding joints and preferential nucleotide insertions at VH--DJH signal joints of excision products of immunoglobulin heavy chain gene rearrangements.

T Shimizu 1, H Yamagishi 1
PMCID: PMC556964  PMID: 1464314

Abstract

During B cell differentiation immunoglobulin (Ig) DH segments join to JH segments, followed by joining of VH to DJH. Although circular excision products of DH--JH rearrangements have been characterized, excision products of VH to DJH joining have never been isolated. We selectively denatured chromosomal DNA of mouse splenocytes and enriched circular DNA spanning the long distance between VH and DH. Subsequent PCR amplifications allowed the identification of signal joints of VH to DJH. Sequence analysis indicated that preexisting DH--JH coding joints of excision products showed a strong bias for reading frame 1, and the absence of reading frame 2, which would allow the expression of a truncated mu chain called D mu protein. When comparing the joints of the VH--DJH and DH--JH rearrangements we observed N-nucleotide insertions to be abundant at the VH--DH signal joint, but very sparse at the DH--JH signal joint, while the coding joints of both contained abundant N-insertions. These differences in N region insertions at the signal joints suggest a differential control of the D--J and V--DJ rearrangements.

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Selected References

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  1. Asarnow D. M., Kuziel W. A., Bonyhadi M., Tigelaar R. E., Tucker P. W., Allison J. P. Limited diversity of gamma delta antigen receptor genes of Thy-1+ dendritic epidermal cells. Cell. 1988 Dec 2;55(5):837–847. doi: 10.1016/0092-8674(88)90139-0. [DOI] [PubMed] [Google Scholar]
  2. Bangs L. A., Sanz I. E., Teale J. M. Comparison of D, JH, and junctional diversity in the fetal, adult, and aged B cell repertoires. J Immunol. 1991 Mar 15;146(6):1996–2004. [PubMed] [Google Scholar]
  3. Bogue M., Candéias S., Benoist C., Mathis D. A special repertoire of alpha:beta T cells in neonatal mice. EMBO J. 1991 Dec;10(12):3647–3654. doi: 10.1002/j.1460-2075.1991.tb04931.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brodeur P. H., Osman G. E., Mackle J. J., Lalor T. M. The organization of the mouse Igh-V locus. Dispersion, interspersion, and the evolution of VH gene family clusters. J Exp Med. 1988 Dec 1;168(6):2261–2278. doi: 10.1084/jem.168.6.2261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carroll S. M., Gaudray P., De Rose M. L., Emery J. F., Meinkoth J. L., Nakkim E., Subler M., Von Hoff D. D., Wahl G. M. Characterization of an episome produced in hamster cells that amplify a transfected CAD gene at high frequency: functional evidence for a mammalian replication origin. Mol Cell Biol. 1987 May;7(5):1740–1750. doi: 10.1128/mcb.7.5.1740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Elliott J. F., Rock E. P., Patten P. A., Davis M. M., Chien Y. H. The adult T-cell receptor delta-chain is diverse and distinct from that of fetal thymocytes. Nature. 1988 Feb 18;331(6157):627–631. doi: 10.1038/331627a0. [DOI] [PubMed] [Google Scholar]
  7. Feeney A. J. Lack of N regions in fetal and neonatal mouse immunoglobulin V-D-J junctional sequences. J Exp Med. 1990 Nov 1;172(5):1377–1390. doi: 10.1084/jem.172.5.1377. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ferrier P., Krippl B., Blackwell T. K., Furley A. J., Suh H., Winoto A., Cook W. D., Hood L., Costantini F., Alt F. W. Separate elements control DJ and VDJ rearrangement in a transgenic recombination substrate. EMBO J. 1990 Jan;9(1):117–125. doi: 10.1002/j.1460-2075.1990.tb08087.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fujimoto S., Yamagishi H. Isolation of an excision product of T-cell receptor alpha-chain gene rearrangements. Nature. 1987 May 21;327(6119):242–243. doi: 10.1038/327242a0. [DOI] [PubMed] [Google Scholar]
  10. Gerondakis S., Bernard O., Cory S., Adams J. M. Immunoglobulin JH rearrangement in a T-cell line reflects fusion to the DH locus at a sequence lacking the nonamer recognition signal. Immunogenetics. 1988;28(4):255–259. doi: 10.1007/BF00345502. [DOI] [PubMed] [Google Scholar]
  11. Gregoire K. E., Goldschneider I., Barton R. W., Bollum F. J. Ontogeny of terminal deoxynucleotidyl transferase-positive cells in lymphohemopoietic tissues of rat and mouse. J Immunol. 1979 Sep;123(3):1347–1352. [PubMed] [Google Scholar]
  12. Griffin B. E., Björck E., Bjursell G., Lindahl T. Sequence complexity of circular Epstein-Bar virus DNA in transformed cells. J Virol. 1981 Oct;40(1):11–19. doi: 10.1128/jvi.40.1.11-19.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gu H., Förster I., Rajewsky K. Sequence homologies, N sequence insertion and JH gene utilization in VHDJH joining: implications for the joining mechanism and the ontogenetic timing of Ly1 B cell and B-CLL progenitor generation. EMBO J. 1990 Jul;9(7):2133–2140. doi: 10.1002/j.1460-2075.1990.tb07382.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gu H., Kitamura D., Rajewsky K. B cell development regulated by gene rearrangement: arrest of maturation by membrane-bound D mu protein and selection of DH element reading frames. Cell. 1991 Apr 5;65(1):47–54. doi: 10.1016/0092-8674(91)90406-o. [DOI] [PubMed] [Google Scholar]
  15. Harada K., Yamagishi H. Lack of feedback inhibition of V kappa gene rearrangement by productively rearranged alleles. J Exp Med. 1991 Feb 1;173(2):409–415. doi: 10.1084/jem.173.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ichihara Y., Hayashida H., Miyazawa S., Kurosawa Y. Only DFL16, DSP2, and DQ52 gene families exist in mouse immunoglobulin heavy chain diversity gene loci, of which DFL16 and DSP2 originate from the same primordial DH gene. Eur J Immunol. 1989 Oct;19(10):1849–1854. doi: 10.1002/eji.1830191014. [DOI] [PubMed] [Google Scholar]
  17. Iwasato T., Arakawa H., Shimizu A., Honjo T., Yamagishi H. Biased distribution of recombination sites within S regions upon immunoglobulin class switch recombination induced by transforming growth factor beta and lipopolysaccharide. J Exp Med. 1992 Jun 1;175(6):1539–1546. doi: 10.1084/jem.175.6.1539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Iwasato T., Shimizu A., Honjo T., Yamagishi H. Circular DNA is excised by immunoglobulin class switch recombination. Cell. 1990 Jul 13;62(1):143–149. doi: 10.1016/0092-8674(90)90248-d. [DOI] [PubMed] [Google Scholar]
  19. Iwasato T., Yamagishi H. Novel excision products of T cell receptor gamma gene rearrangements and developmental stage specificity implied by the frequency of nucleotide insertions at signal joints. Eur J Immunol. 1992 Jan;22(1):101–106. doi: 10.1002/eji.1830220116. [DOI] [PubMed] [Google Scholar]
  20. Kurosawa Y., Tonegawa S. Organization, structure, and assembly of immunoglobulin heavy chain diversity DNA segments. J Exp Med. 1982 Jan 1;155(1):201–218. doi: 10.1084/jem.155.1.201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lafaille J. J., DeCloux A., Bonneville M., Takagaki Y., Tonegawa S. Junctional sequences of T cell receptor gamma delta genes: implications for gamma delta T cell lineages and for a novel intermediate of V-(D)-J joining. Cell. 1989 Dec 1;59(5):859–870. doi: 10.1016/0092-8674(89)90609-0. [DOI] [PubMed] [Google Scholar]
  22. Lawler A. M., Lin P. S., Gearhart P. J. Adult B-cell repertoire is biased toward two heavy-chain variable-region genes that rearrange frequently in fetal pre-B cells. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2454–2458. doi: 10.1073/pnas.84.8.2454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lennon G. G., Perry R. P. Identification of a defective mouse immunoglobulin D (diversity) element which can undergo DJH, but not VHD, recombination. Immunogenetics. 1989;30(5):383–386. doi: 10.1007/BF02425279. [DOI] [PubMed] [Google Scholar]
  24. Lieber M. R., Hesse J. E., Mizuuchi K., Gellert M. Lymphoid V(D)J recombination: nucleotide insertion at signal joints as well as coding joints. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8588–8592. doi: 10.1073/pnas.85.22.8588. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Livant D., Blatt C., Hood L. One heavy chain variable region gene segment subfamily in the BALB/c mouse contains 500-1000 or more members. Cell. 1986 Nov 7;47(3):461–470. doi: 10.1016/0092-8674(86)90603-3. [DOI] [PubMed] [Google Scholar]
  26. Malynn B. A., Yancopoulos G. D., Barth J. E., Bona C. A., Alt F. W. Biased expression of JH-proximal VH genes occurs in the newly generated repertoire of neonatal and adult mice. J Exp Med. 1990 Mar 1;171(3):843–859. doi: 10.1084/jem.171.3.843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Matsuda F., Lee K. H., Nakai S., Sato T., Kodaira M., Zong S. Q., Ohno H., Fukuhara S., Honjo T. Dispersed localization of D segments in the human immunoglobulin heavy-chain locus. EMBO J. 1988 Apr;7(4):1047–1051. doi: 10.1002/j.1460-2075.1988.tb02912.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Meek K. Analysis of junctional diversity during B lymphocyte development. Science. 1990 Nov 9;250(4982):820–823. doi: 10.1126/science.2237433. [DOI] [PubMed] [Google Scholar]
  29. Nakanishi K., Sugimura K., Yaoita Y., Maeda K., Kashiwamura S., Honjo T., Kishimoto T. A T15-idiotype-positive T suppressor hybridoma does not use the T15 VH gene segment. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6984–6988. doi: 10.1073/pnas.79.22.6984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nelson K. J., Haimovich J., Perry R. P. Characterization of productive and sterile transcripts from the immunoglobulin heavy-chain locus: processing of micron and muS mRNA. Mol Cell Biol. 1983 Jul;3(7):1317–1332. doi: 10.1128/mcb.3.7.1317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Neuberger M. S. Expression and regulation of immunoglobulin heavy chain gene transfected into lymphoid cells. EMBO J. 1983;2(8):1373–1378. doi: 10.1002/j.1460-2075.1983.tb01594.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Opstelten D., Deenen G. J., Rozing J., Hunt S. V. B lymphocyte-associated antigens on terminal deoxynucleotidyl transferase-positive cells and pre-B cells in bone marrow of the rat. J Immunol. 1986 Jul 1;137(1):76–84. [PubMed] [Google Scholar]
  33. Pardoll D. M., Fowlkes B. J., Bluestone J. A., Kruisbeek A., Maloy W. L., Coligan J. E., Schwartz R. H. Differential expression of two distinct T-cell receptors during thymocyte development. Nature. 1987 Mar 5;326(6108):79–81. doi: 10.1038/326079a0. [DOI] [PubMed] [Google Scholar]
  34. Reth M. G., Alt F. W. Novel immunoglobulin heavy chains are produced from DJH gene segment rearrangements in lymphoid cells. 1984 Nov 29-Dec 5Nature. 312(5993):418–423. doi: 10.1038/312418a0. [DOI] [PubMed] [Google Scholar]
  35. Reth M. G., Jackson S., Alt F. W. VHDJH formation and DJH replacement during pre-B differentiation: non-random usage of gene segments. EMBO J. 1986 Sep;5(9):2131–2138. doi: 10.1002/j.1460-2075.1986.tb04476.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rolink A., Melchers F. Molecular and cellular origins of B lymphocyte diversity. Cell. 1991 Sep 20;66(6):1081–1094. doi: 10.1016/0092-8674(91)90032-t. [DOI] [PubMed] [Google Scholar]
  37. Rothenberg E., Triglia D. Clonal proliferation unlinked to terminal deoxynucleotidyl transferase synthesis in thymocytes of young mice. J Immunol. 1983 Apr;130(4):1627–1633. [PubMed] [Google Scholar]
  38. Rush M. G., Misra R. Extrachromosomal DNA in eucaryotes. Plasmid. 1985 Nov;14(3):177–191. doi: 10.1016/0147-619x(85)90001-0. [DOI] [PubMed] [Google Scholar]
  39. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  40. Sakano H., Maki R., Kurosawa Y., Roeder W., Tonegawa S. Two types of somatic recombination are necessary for the generation of complete immunoglobulin heavy-chain genes. Nature. 1980 Aug 14;286(5774):676–683. doi: 10.1038/286676a0. [DOI] [PubMed] [Google Scholar]
  41. Sanger F. Determination of nucleotide sequences in DNA. Science. 1981 Dec 11;214(4526):1205–1210. doi: 10.1126/science.7302589. [DOI] [PubMed] [Google Scholar]
  42. Stanfield S., Helinski D. R. Small circular DNA in Drosophila melanogaster. Cell. 1976 Oct;9(2):333–345. doi: 10.1016/0092-8674(76)90123-9. [DOI] [PubMed] [Google Scholar]
  43. Takeshita S., Toda M., Yamagishi H. Excision products of the T cell receptor gene support a progressive rearrangement model of the alpha/delta locus. EMBO J. 1989 Nov;8(11):3261–3270. doi: 10.1002/j.1460-2075.1989.tb08486.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Toda M., Hirama T., Takeshita S., Yamagishi H. Excision products of immunoglobulin gene rearrangements. Immunol Lett. 1989 Jun 15;21(4):311–316. doi: 10.1016/0165-2478(89)90025-4. [DOI] [PubMed] [Google Scholar]
  45. Tonegawa S. Somatic generation of antibody diversity. Nature. 1983 Apr 14;302(5909):575–581. doi: 10.1038/302575a0. [DOI] [PubMed] [Google Scholar]
  46. Tsubata T., Tsubata R., Reth M. Cell surface expression of the short immunoglobulin mu chain (D mu protein) in murine pre-B cells is differently regulated from that of the intact mu chain. Eur J Immunol. 1991 Jun;21(6):1359–1363. doi: 10.1002/eji.1830210605. [DOI] [PubMed] [Google Scholar]
  47. Usuda S., Takemori T., Matsuoka M., Shirasawa T., Yoshida K., Mori A., Ishizaka K., Sakano H. Immunoglobulin V gene replacement is caused by the intramolecular DNA deletion mechanism. EMBO J. 1992 Feb;11(2):611–618. doi: 10.1002/j.1460-2075.1992.tb05093.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Yamagishi H., Tsuda T., Fujimoto S., Toda M., Kato K., Maekawa Y., Umeno M., Anai M. Purification of small polydisperse circular DNA of eukaryotic cells by use of ATP-dependent deoxyribonuclease. Gene. 1983 Dec;26(2-3):317–321. doi: 10.1016/0378-1119(83)90205-6. [DOI] [PubMed] [Google Scholar]
  49. Yancopoulos G. D., Alt F. W. Regulation of the assembly and expression of variable-region genes. Annu Rev Immunol. 1986;4:339–368. doi: 10.1146/annurev.iy.04.040186.002011. [DOI] [PubMed] [Google Scholar]
  50. Yancopoulos G. D., Desiderio S. V., Paskind M., Kearney J. F., Baltimore D., Alt F. W. Preferential utilization of the most JH-proximal VH gene segments in pre-B-cell lines. Nature. 1984 Oct 25;311(5988):727–733. doi: 10.1038/311727a0. [DOI] [PubMed] [Google Scholar]
  51. Yaoita Y., Matsunami N., Choi C. Y., Sugiyama H., Kishimoto T., Honjo T. The D-JH complex is an intermediate to the complete immunoglobulin heavy-chain V-region gene. Nucleic Acids Res. 1983 Nov 11;11(21):7303–7316. doi: 10.1093/nar/11.21.7303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Yaoita Y., Takahashi M., Azuma C., Kanai Y., Honjo T. Biased expression of variable region gene families of the immunoglobulin heavy chain in autoimmune-prone mice. J Biochem. 1988 Sep;104(3):337–343. doi: 10.1093/oxfordjournals.jbchem.a122470. [DOI] [PubMed] [Google Scholar]

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