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. 1985 May;4(5):1225–1230. doi: 10.1002/j.1460-2075.1985.tb03764.x

Functional and pseudogenes are similarly organized and may equally contribute to the extensive antibody diversity of the IgVHII family.

C Schiff, M Milili, M Fougereau
PMCID: PMC554328  PMID: 3924600

Abstract

Eleven germ-line immunoglobulin VH genes have been isolated from a BALB/c genomic library, using a cDNA probe specific for the GAT/NPa variable region. Restriction fragments of all genes were sequenced: two over 800 bp, covering signals of the 5'- and 3'-non-coding regions, three encompassing the complete coding region and part of the 5', the remaining sequences covering most of the V coding region. All sequences pertained to the VHII family, and were compared with the other 13 homologous genes already published. Characteristic features defining the family are clearly visible all along the sequences analyzed, including the 5'-non-coding region, the leader fragment and the intron organization. About half of the compared genes have pseudogene characteristics, defined either by a stop codon in the coding region or the lack of an initiator codon in the leader segment. Analysis of the replacement mutations, as compared with silent ones, indicate that they are highly clustered in complementarity determining regions, for both the functional and the pseudogenes, suggesting that all genes have been submitted to similar selective pressure, and that the pseudogene repertoire may be actively used, by recombination and/or conversion process. Signals that regulate transcription are highly conserved through the family barriers. The VHII group is the largest Ig V genes family, with extreme sequence divergences reaching 22% nucleotide differences. As no two genes were found identical out of the 24 members compared, and as two genes were found to differ by as little as three nucleotides, it seems that the previous estimate of 60 members might be much too low.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alt F. W., Baltimore D. Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4118–4122. doi: 10.1073/pnas.79.13.4118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amzel L. M., Poljak R. J., Saul F., Varga J. M., Richards F. F. The three dimensional structure of a combining region-ligand complex of immunoglobulin NEW at 3.5-A resolution. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1427–1430. doi: 10.1073/pnas.71.4.1427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Banerji J., Olson L., Schaffner W. A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell. 1983 Jul;33(3):729–740. doi: 10.1016/0092-8674(83)90015-6. [DOI] [PubMed] [Google Scholar]
  4. Benoist C., O'Hare K., Breathnach R., Chambon P. The ovalbumin gene-sequence of putative control regions. Nucleic Acids Res. 1980 Jan 11;8(1):127–142. doi: 10.1093/nar/8.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bentley D. L., Rabbitts T. H. Human V kappa immunoglobulin gene number: implications for the origin of antibody diversity. Cell. 1981 Jun;24(3):613–623. doi: 10.1016/0092-8674(81)90088-x. [DOI] [PubMed] [Google Scholar]
  6. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  7. Blankenstein T., Zoebelein G., Krawinkel U. Analysis of immunoglobulin heavy chain V-region genes belonging to the V NP-gene family. Nucleic Acids Res. 1984 Sep 11;12(17):6887–6900. doi: 10.1093/nar/12.17.6887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bothwell A. L., Paskind M., Reth M., Imanishi-Kari T., Rajewsky K., Baltimore D. Heavy chain variable region contribution to the NPb family of antibodies: somatic mutation evident in a gamma 2a variable region. Cell. 1981 Jun;24(3):625–637. doi: 10.1016/0092-8674(81)90089-1. [DOI] [PubMed] [Google Scholar]
  9. Brack C., Hirama M., Lenhard-Schuller R., Tonegawa S. A complete immunoglobulin gene is created by somatic recombination. Cell. 1978 Sep;15(1):1–14. doi: 10.1016/0092-8674(78)90078-8. [DOI] [PubMed] [Google Scholar]
  10. Breathnach R., Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. doi: 10.1146/annurev.bi.50.070181.002025. [DOI] [PubMed] [Google Scholar]
  11. Brodeur P. H., Riblet R. The immunoglobulin heavy chain variable region (Igh-V) locus in the mouse. I. One hundred Igh-V genes comprise seven families of homologous genes. Eur J Immunol. 1984 Oct;14(10):922–930. doi: 10.1002/eji.1830141012. [DOI] [PubMed] [Google Scholar]
  12. Clarke C., Berenson J., Goverman J., Boyer P. D., Crews S., Siu G., Calame K. An immunoglobulin promoter region is unaltered by DNA rearrangement and somatic mutation during B-cell development. Nucleic Acids Res. 1982 Dec 11;10(23):7731–7749. doi: 10.1093/nar/10.23.7731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Clarke S. H., Claflin J. L., Rudikoff S. Polymorphism in immunoglobulin heavy chains suggesting gene conversion. Proc Natl Acad Sci U S A. 1982 May;79(10):3280–3284. doi: 10.1073/pnas.79.10.3280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Cohen J. B., Effron K., Rechavi G., Ben-Neriah Y., Zakut R., Givol D. Simple DNA sequences in homologous flanking regions near immunoglobulin VH genes: a role in gene interaction? Nucleic Acids Res. 1982 Jun 11;10(11):3353–3370. doi: 10.1093/nar/10.11.3353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Cohen J. B., Givol D. Conservation and divergence of immunoglobulin VH pseudogenes. EMBO J. 1983;2(10):1795–1800. doi: 10.1002/j.1460-2075.1983.tb01660.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Crews S., Griffin J., Huang H., Calame K., Hood L. A single VH gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. Cell. 1981 Jul;25(1):59–66. doi: 10.1016/0092-8674(81)90231-2. [DOI] [PubMed] [Google Scholar]
  17. De Préval C., Fougereau M. Specific interaction between VH and VL regions of human monoclonal immunoglobulins. J Mol Biol. 1976 Apr 15;102(3):657–678. doi: 10.1016/0022-2836(76)90340-5. [DOI] [PubMed] [Google Scholar]
  18. Early P., Huang H., Davis M., Calame K., Hood L. An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell. 1980 Apr;19(4):981–992. doi: 10.1016/0092-8674(80)90089-6. [DOI] [PubMed] [Google Scholar]
  19. Falkner F. G., Zachau H. G. Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements. Nature. 1984 Jul 5;310(5972):71–74. doi: 10.1038/310071a0. [DOI] [PubMed] [Google Scholar]
  20. Gillies S. D., Morrison S. L., Oi V. T., Tonegawa S. A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell. 1983 Jul;33(3):717–728. doi: 10.1016/0092-8674(83)90014-4. [DOI] [PubMed] [Google Scholar]
  21. Givol D., Zakut R., Effron K., Rechavi G., Ram D., Cohen J. B. Diversity of germ-line immunoglobulin VH genes. Nature. 1981 Jul 30;292(5822):426–430. doi: 10.1038/292426a0. [DOI] [PubMed] [Google Scholar]
  22. Griffiths G. M., Berek C., Kaartinen M., Milstein C. Somatic mutation and the maturation of immune response to 2-phenyl oxazolone. Nature. 1984 Nov 15;312(5991):271–275. doi: 10.1038/312271a0. [DOI] [PubMed] [Google Scholar]
  23. Kabat E. A., Wu T. T. Attempts to locate complementarity-determining residues in the variable positions of light and heavy chains. Ann N Y Acad Sci. 1971 Dec 31;190:382–393. doi: 10.1111/j.1749-6632.1971.tb13550.x. [DOI] [PubMed] [Google Scholar]
  24. Kabat E. A., Wu T. T., Bilofsky H. Variable region genes for the immunoglobulin framework are assembled from small segments of DNA--a hypothesis. Proc Natl Acad Sci U S A. 1978 May;75(5):2429–2433. doi: 10.1073/pnas.75.5.2429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kataoka T., Nikaido T., Miyata T., Moriwaki K., Honjo T. The nucleotide sequences of rearranged and germline immunoglobulin VH genes of a mouse myeloma MC101 and evolution of VH genes in mouse. J Biol Chem. 1982 Jan 10;257(1):277–285. [PubMed] [Google Scholar]
  26. Krawinkel U., Zoebelein G., Brüggemann M., Radbruch A., Rajewsky K. Recombination between antibody heavy chain variable-region genes: evidence for gene conversion. Proc Natl Acad Sci U S A. 1983 Aug;80(16):4997–5001. doi: 10.1073/pnas.80.16.4997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Loh D. Y., Bothwell A. L., White-Scharf M. E., Imanishi-Kari T., Baltimore D. Molecular basis of a mouse strain-specific anti-hapten response. Cell. 1983 May;33(1):85–93. doi: 10.1016/0092-8674(83)90337-9. [DOI] [PubMed] [Google Scholar]
  28. Matthyssens G., Rabbitts T. H. Structure and multiplicity of genes for the human immunoglobulin heavy chain variable region. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6561–6565. doi: 10.1073/pnas.77.11.6561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Max E. E., Seidman J. G., Leder P. Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3450–3454. doi: 10.1073/pnas.76.7.3450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  31. Milstein C., Brownlee G. G., Harrison T. M., Mathews M. B. A possible precursor of immunoglobulin light chains. Nat New Biol. 1972 Sep 27;239(91):117–120. doi: 10.1038/newbio239117a0. [DOI] [PubMed] [Google Scholar]
  32. Ollo R., Auffray C., Sikorav J. L., Rougeon F. Mouse heavy chain variable regions: nucleotide sequence of a germ-line VH gene segment. Nucleic Acids Res. 1981 Aug 25;9(16):4099–4109. doi: 10.1093/nar/9.16.4099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ollo R., Rougeon F. Gene conversion and polymorphism: generation of mouse immunoglobulin gamma 2a chain alleles by differential gene conversion by gamma 2b chain gene. Cell. 1983 Feb;32(2):515–523. doi: 10.1016/0092-8674(83)90471-3. [DOI] [PubMed] [Google Scholar]
  34. Ollo R., Sikorav J. L., Rougeon F. Structural relationships among mouse and human immunoglobulin VH genes in the subgroup III. Nucleic Acids Res. 1983 Nov 25;11(22):7887–7897. doi: 10.1093/nar/11.22.7887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Parslow T. G., Blair D. L., Murphy W. J., Granner D. K. Structure of the 5' ends of immunoglobulin genes: a novel conserved sequence. Proc Natl Acad Sci U S A. 1984 May;81(9):2650–2654. doi: 10.1073/pnas.81.9.2650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Queen C., Baltimore D. Immunoglobulin gene transcription is activated by downstream sequence elements. Cell. 1983 Jul;33(3):741–748. doi: 10.1016/0092-8674(83)90016-8. [DOI] [PubMed] [Google Scholar]
  37. Rechavi G., Ram D., Glazer L., Zakut R., Givol D. Evolutionary aspects of immunoglobulin heavy chain variable region (VH) gene subgroups. Proc Natl Acad Sci U S A. 1983 Feb;80(3):855–859. doi: 10.1073/pnas.80.3.855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sakano H., Hüppi K., Heinrich G., Tonegawa S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979 Jul 26;280(5720):288–294. doi: 10.1038/280288a0. [DOI] [PubMed] [Google Scholar]
  39. Sakano H., Kurosawa Y., Weigert M., Tonegawa S. Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes. Nature. 1981 Apr 16;290(5807):562–565. doi: 10.1038/290562a0. [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., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Schiff C., Milili M., Fougereau M. Immunoglobulin diversity: analysis of the germ-line VH gene repertoire of the murine anti-GAT response. Nucleic Acids Res. 1983 Jun 25;11(12):4007–4017. doi: 10.1093/nar/11.12.4007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Schreier P. H., Bothwell A. L., Mueller-Hill B., Baltimore D. Multiple differences between the nucleic acid sequences of the IgG2aa and IgG2ab alleles of the mouse. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4495–4499. doi: 10.1073/pnas.78.7.4495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Seidman J. G., Leder A., Nau M., Norman B., Leder P. Antibody diversity. Science. 1978 Oct 6;202(4363):11–17. doi: 10.1126/science.99815. [DOI] [PubMed] [Google Scholar]
  45. Seidman J. G., Max E. E., Leder P. A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation. Nature. 1979 Aug 2;280(5721):370–375. doi: 10.1038/280370a0. [DOI] [PubMed] [Google Scholar]

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