Abstract
Organization of the IGHV genes (n=108) on single human chromosomes has been determined by detecting these sequences in single sperm using multiplex PCR amplification followed by microarray detection. A total of 374 single sperm samples from five Caucasian males were studied. Three deletion/insertion polymorphisms (Del I–Del III) with deletion allele frequencies ranging from 0.1 to 0.3 were identified. Del I is a previously reported polymorphism affecting three IGHV genes (IGHV1–8, IGHV3–9, and IGHV2–10). Del II affects a region 2–18 kb containing two pseudogenes IGHV(II)-28.1 and IGHV3–29, and Del III spans ∼21–53 kb involving genes IGHV4–39, IGHV7–40, IGHV(II)-40-1, and IGHV3–41. Deletion alleles of both Dels II and III were found in a heterozygous state, and therefore, could not be easily detected if haploid samples were not used in the study. Results of the present study indicate that deletions/insertions together with other possible chromosomal rearrangements may play an important role in forming the genetic structure of the IGHV region, and may significantly contribute to antibody diversity. Since these three polymorphisms are located within or next to the 3′ half of the IGHV region, they may have an important role in the expressed IGHV gene repertoire during immune response.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 6 digital issues and online access to articles
$119.00 per year
only $19.83 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Croce CM, Shander M, Martinis J et al. Chromosomal location of the genes for human immunoglobulin heavy chains. Proc Natl Acad Sci USA 1979; 76: 3416–3419.
Cox DW, Markovic VD, Teshima IE . Genes for immunoglobulin heavy chains and for alpha 1-antitrypsin are localized to specific regions of chromosome 14q. Nature 1982; 297: 428–430.
Kirsch IR, Morton CC, Nakahara K, Leder P . Human immunoglobulin heavy chain genes map to a region of translocations in malignant B lymphocytes. Science 1982; 216: 301–303.
Cherif D, Berger R . New localizations of VH sequences by in situ hybridization with biotinylated probes. Genes Chromosomes Cancer 1990; 2: 103–108.
Matsuda F, Shin EK, Hirabayashi Y, Nagaoka H . Organization of variable region segments of the human immunoglobulin heavy chain: duplication of the D5 cluster within the locus and interchromosomal translocation of variable region segments. EMBO J 1990; 9: 2501–2506.
Tomlinson IM, Cook GP, Carter NP et al. Human immunoglobulin VH and D segments on chromosomes 15q11.2 and 16p11.2. Hum Mol Genet 1994; 3: 853–860.
Tomlinson IM, Walter G, Marks JD, Llewelyn MB, Winter G . The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops. J Mol Biol 1992; 227: 776–798.
Cook GP, Tomlinson IM, Walter G et al. A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14q. Nat Genet 1994; 7: 162–168.
Williams SC, Frippiat JP, Tomlinson IM, Ignatovich O, Lefranc MP, Winter G . Sequence and evolution of the human germline V lambda repertoire. J Mol Biol 1996; 264: 220–232.
Matsuda F, Shin EK, Nagaoka H et al. Structure and physical map of 64 variable segments in the 3′0.8-megabase region of the human immunoglobulin heavy-chain locus. Nat Genet 1993; 3: 88–94.
Matsuda F, Ishii K, Bourvagnet P et al. The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus. J Exp Med 1998; 188: 2151–2162.
Walter G, Tomlinson IM, Cook GP, Winter G, Rabbitts TH, Dear PH . HAPPY mapping of a YAC reveals alternative haplotypes in the human immunoglobulin VH locus. Nucleic Acids Res 1993; 21: 4524–4529.
Tonegawa S . Somatic generation of antibody diversity. Nature 1983; 302: 575–581.
Honjo T, Habu S . Origin of immune diversity: genetic variation and selection. Annu Rev Biochem 1985; 54: 803–830.
Berek C, Milstein C . The dynamic nature of the antibody repertoire. Immunol Rev 1988; 105: 5–26.
Jacob J, Kelsoe G, Rajewsky K, Weiss U . Intraclonal generation of antibody mutants in germinal centres. Nature 1991; 354: 389–392.
Pham P, Bransteitter R, Petruska J, Goodman MF . Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 2003; 424: 103–107.
Nagaoka H, Muramatsu M, Yamamura N, Kinoshita K, Honjo T . Activation-induced deaminase (AID)-directed hypermutation in the immunoglobulin Smu region: implication of AID involvement in a common step of class switch recombination and somatic hypermutation. J Exp Med 2002; 195: 529–534.
Jung D, Alt FW . Unraveling V(D)J recombination; insights into gene regulation. Cell 2004; 116: 299–311.
Cui X, Li H . Human immunoglobulin VH4 sequences resolved by population-based analysis after enzymatic amplification and denaturing gradient gel electrophoresis. Eur J Immunogenet 2000; 27: 37–46.
Cui X, Li H . Determination of gene organization in individual haplotypes by analyzing single DNA fragments from single spermatozoa. Proc Natl Acad Sci USA 1998; 95: 10791–10796.
Cui X, Li H . Discriminating between allelic and interlocus differences among human immunoglobulin VH4 sequences by analyzing single spermatozoa. Hum Genet 1997; 100: 96–100.
Li H, Cui X, Pramanik S, Chimge NO . Genetic diversity of the human immunoglobulin heavy chain VH region. Immunol Rev 2002; 190: 53–68.
Pramanik S, Li H . Direct detection of insertion/deletion polymorphisms in an autosomal region by analyzing high-density markers in individual spermatozoa. Am J Hum Genet 2002; 71: 1342–1352.
Lefranc M-P, Lefranc G . The Immunoglobulin Factsbook, Vol. xiv, Academic Press, San Diego, 2001, p. 457.
Li H, Hood L . Multiplex genotype determination at a DNA sequence polymorphism cluster in the human immunoglobulin heavy-chain region. Genomics 1995; 26: 199–206.
den Dunnen JT, Antonarakis SE . Nomenclature for the description of human sequence variations. Hum Genet 2001; 109: 121–124.
Shin EK, Matsuda F, Nagaoka H et al. Physical map of the 3′ region of the human immunoglobulin heavy chain locus: clustering of autoantibody-related variable segments in one haplotype. EMBO J 1991; 10: 3641–3645.
Chen PP, Yang PM . A segment of human Vh gene locus is duplicated. Scand J Immunol 1990; 31: 593–599.
Yang PM, Olsen NJ, Siminovitch KA et al. Possible deletion of a developmentally regulated heavy-chain variable region gene in autoimmune diseases. Proc Natl Acad Sci USA 1990; 87: 7907–7911.
Sasso EH, Willems van Dijk K, Bull A, van der Maarel SM, Milner EC . VH genes in tandem array comprise a repeated germline motif. J Immunol 1992; 149: 1230–1236.
Milner EC, Hufnagle WO, Glas AM, Suzuki I, Alexander C . Polymorphism and utilization of human VH Genes. Ann NY Acad Sci 1995; 764: 50–61.
Tomlinson IM, Williams SC, Ignatovich O, Corbett SJ, Winter G . Vbase sequence directory, MRC Centre for Protein Engineering, 1998.
Walter MA, Dosch HM, Cox DW . A deletion map of the human immunoglobulin heavy chain variable region. J Exp Med 1991; 174: 335–349.
Ghanem N, Dariavach P, Bensmana M, Chibani J, Lefranc G, Lefranc MP . Polymorphism of immunoglobulin lambda constant region genes in populations from France, Lebanon and Tunisia. Exp Clin Immunogenet 1988; 5: 186–195.
Taub RA, Hollis GF, Hieter PA, Korsmeyer S, Waldmann TA, Leder P . Variable amplification of immunoglobulin lambda light-chain genes in human populations. Nature 1983; 304: 172–174.
Schaible G, Rappold GA, Pargent W, Zachau HG . The immunoglobulin kappa locus: polymorphism and haplotypes of Caucasoid and non-Caucasoid individuals. Hum Genet 1993; 91: 261–267.
Ghanem N, Buresi C, Moisan JP et al. Deletion, insertion, and restriction site polymorphism of the T-cell receptor gamma variable locus in French, Lebanese, Tunisian, and black African populations. Immunogenetics 1989; 30: 350–360.
Ghanem N, Soua Z, Zhang XG et al. Polymorphism of the T-cell receptor gamma variable and constant region genes in a Chinese population. Hum Genet 1991; 86: 450–456.
Bohme J, Andersson M, Andersson G, Moller E, Peterson PA, Rask L . HLA-DR beta genes vary in number between different DR specificities, whereas the number of DQ beta genes is constant. J Immunol 1985; 135: 2149–2155.
Tokunaga K, Saueracker G, Kay PH, Christiansen FT, Anand R, Dawkins RL . Extensive deletions and insertions in different MHC supratypes detected by pusled field gel electrophoresis. J Exp Med 1988; 168: 933–940.
Martin MP, Bashirova A, Traherne J, Trowsdale J, Carrington M . Cutting edge: expansion of the KIR locus by unequal crossing over. J Immunol 2003; 171: 2192–2195.
Hikami K, Tsuchiya N, Yabe T, Tokunaga K . Variations of human killer cell lectin-like receptors: common occurrence of NKG2-C deletion in the general population. Genes Immun 2003; 4: 160–167.
Lefranc MP, Lefranc G, Rabbitts TH . Inherited deletion of immunoglobulin heavy chain constant region genes in normal human individuals. Nature 1982; 300: 760–762.
Migone N, Oliviero S, de Lange G et al. Multiple gene deletions within the human immunoglobulin heavy-chain cluster. Proc Natl Acad Sci USA 1984; 81: 5811–5815.
Brusco A, Cinque F, Saviozzi S, Boccazzi C, De Marchi M, Carbonara AO . The G4 gene is duplicated in 44% of human immunoglobulin heavy chain constant region haplotypes. Hum Genet 1997; 100: 84–89.
Brusco A, Cariota U, Bottaro A et al. Variability of the immunoglobulin heavy chain constant region locus: a population study. Hum Genet 1995; 95: 319–326.
Bech-Hansen NT, Cox DW . Duplication of the human immunoglobulin heavy chain gamma 2 gene. Am J Hum Genet 1986; 38: 67–74.
Olsson PG, Rabbani H, Hammarstrom L, Smith CI . Novel human immunoglobulin heavy chain constant region gene deletion haplotypes characterized by pulsed-field electrophoresis. Clin Exp Immunol 1993; 94: 84–90.
Cui XF, Li HH, Goradia TM et al. Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers. Proc Natl Acad Sci USA 1989; 86: 9389–9393.
Acknowledgements
We thank Dr Marco Azaro for help in preparation of illustrations, Drs Weichung Shih, Hui-Yun Wang and Xiangfeng Cui for helpful discussions and experimental help, and Danielle M Frikker for her comments on the paper. This work was supported in part by a grant (R01 AI045956) from the National Institute of Allergy and Infectious Diseases, NIH to HL.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Chimge, NO., Pramanik, S., Hu, G. et al. Determination of gene organization in the human IGHV region on single chromosomes. Genes Immun 6, 186–193 (2005). https://doi.org/10.1038/sj.gene.6364176
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/sj.gene.6364176
Keywords
This article is cited by
-
Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire
Nature Communications (2023)
-
T cell receptor beta germline variability is revealed by inference from repertoire data
Genome Medicine (2022)
-
Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes
Immunogenetics (2020)
-
On being the right size: antibody repertoire formation in the mouse and human
Immunogenetics (2018)
-
Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region
BMC Genomics (2011)