Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Original Article
  • Published:

Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

Abstract

The human RCCX is a common multiallelic copy number variation locus whose number of segments varies between one and four in a chromosome. The monomodular form normally comprises four functional genes, but in duplicated RCCX segments generally only the gene-encoding complement component C4 produces a protein. C4 genes can code either for a C4A or a C4B isotype protein and exhibit dichotomous size variation. Distinct RCCX variants show association with numerous diseases; however, identification of the basis of these associations is often challenging, not least because the RCCX is localized in the major histocompatibility complex (MHC) region, a genomic area characterized by exceedingly long-range linkage disequilibrium. Here we present a detailed analysis on RCCX variants and their relationship with so-called ‘ancestral’ or ‘conserved extended’ MHC haplotypes in healthy Caucasians. In addition to former investigations, precise order and size of all C4A and C4B genes were determined even in trimodular RCCX structures. Considering C4 copy numbers, length, isotype specificity and CYP21A2 copy numbers, we have identified 15 distinct RCCX variants and described the RCCX structures involved in 29 repeatedly occurring MHC haplotypes. The findings should become a useful tool for future RCCX- and MHC-related disease association studies.

This is a preview of subscription content, access via your institution

Access options

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

Figure 1
Figure 2

Similar content being viewed by others

References

  1. Mack M, Bender K, Schneider PM . Detection of retroviral antisense transcripts and promoter activity of the HERV-K(C4) insertion in the MHC class III region. Immunogenetics 2004; 56: 321–332.

    Article  CAS  Google Scholar 

  2. Blanchong CA, Zhou B, Rupert KL, Chung EK, Jones KN, Sotos JF et al. Deficiencies of human complement component C4A and C4B and heterozygosity in length variants of RP-C4-CYP21-TNX (RCCX) modules in caucasians. The load of RCCX genetic diversity on major histocompatibility complex-associated disease. J Exp Med 2000; 191: 2183–2196.

    Article  CAS  Google Scholar 

  3. Yang Y, Chung EK, Zhou B, Blanchong CA, Yu CY, Fust G et al. Diversity in intrinsic strengths of the human complement system: serum C4 protein concentrations correlate with C4 gene size and polygenic variations, hemolytic activities, and body mass index. J Immunol 2003; 171: 2734–2745.

    Article  CAS  Google Scholar 

  4. Dodds AW, Ren XD, Willis AC, Law SK . The reaction mechanism of the internal thioester in the human complement component C4. Nature 1996; 379: 177–179.

    Article  CAS  Google Scholar 

  5. Yang Y, Chung EK, Zhou B, Lhotta K, Hebert LA, Birmingham DJ et al. The intricate role of complement component C4 in human systemic lupus erythematosus. Curr Dir Autoimmun 2004; 7: 98–132.

    Article  CAS  Google Scholar 

  6. Szilagyi A, Fust G . Diseases associated with the low copy number of the C4B gene encoding C4, the fourth component of complement. Cytogenet Genome Res 2008; 123: 118–130.

    Article  CAS  Google Scholar 

  7. White PC, Speiser PW . Congenital adrenal hyperplasia due to 21-hydroxylase deficiency. Endocr Rev 2000; 21: 245–291.

    CAS  PubMed  Google Scholar 

  8. Brellier F, Tucker RP, Chiquet-Ehrismann R . Tenascins and their implications in diseases and tissue mechanics. Scand J Med Sci Sports 2009; 19: 511–519.

    Article  CAS  Google Scholar 

  9. Lehner B, Semple JI, Brown SE, Counsell D, Campbell RD, Sanderson CM . Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region. Genomics 2004; 83: 153–167.

    Article  CAS  Google Scholar 

  10. Saxena K, Kitzmiller KJ, Wu YL, Zhou B, Esack N, Hiremath L et al. Great genotypic and phenotypic diversities associated with copy-number variations of complement C4 and RP-C4-CYP21-TNX (RCCX) modules: a comparison of Asian-Indian and European American populations. Mol Immunol 2009; 46: 1289–1303.

    Article  CAS  Google Scholar 

  11. Chung EK, Yang Y, Rupert KL, Jones KN, Rennebohm RM, Blanchong CA et al. Determining the one, two, three, or four long and short loci of human complement C4 in a major histocompatibility complex haplotype encoding C4A or C4B proteins. Am J Hum Genet 2002; 71: 810–822.

    Article  Google Scholar 

  12. Yunis EJ, Larsen CE, Fernandez-Vina M, Awdeh ZL, Romero T, Hansen JA et al. Inheritable variable sizes of DNA stretches in the human MHC: conserved extended haplotypes and their fragments or blocks. Tissue Antigens 2003; 62: 1–20.

    Article  CAS  Google Scholar 

  13. Szilagyi A, Banlaki Z, Pozsonyi E, Yunis EJ, Awdeh ZL, Hosso A et al. Frequent occurrence of conserved extended haplotypes (CEHs) in two Caucasian populations. Mol Immunol 2010; 47: 1899–1904.

    Article  CAS  Google Scholar 

  14. Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G et al. Intraspecific evolution of human RCCX copy number variation traced by the haplotypes of CYP21A2 gene. (Submitted).

  15. Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B et al. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 2007; 80: 1037–1054.

    Article  CAS  Google Scholar 

  16. Dorak MT, Shao W, Machulla HK, Lobashevsky ES, Tang J, Park MH et al. Conserved extended haplotypes of the major histocompatibility complex: further characterization. Genes Immun 2006; 7: 450–467.

    Article  CAS  Google Scholar 

  17. Chu X, Braun-Heimer L, Rittner C, Schneider PM . Identification of the recombination site within the steroid 21-hydroxylase gene (CYP21) of the HLA-B47,DR7 haplotype. Exp Clin Immunogenet 1992; 9: 80–85.

    CAS  PubMed  Google Scholar 

  18. Valente FP, Tan C, Phipps M, Witt CS, Kaur G, Gut I et al. TNF block haplotypes associated with conserved MHC haplotypes in European, Asian and Australian Aboriginal donors. Tissue Antigens 2009; 74: 57–61.

    Article  CAS  Google Scholar 

  19. Chung EK, Yang Y, Rennebohm RM, Lokki ML, Higgins GC, Jones KN et al. Genetic sophistication of human complement components C4A and C4B and RP-C4-CYP21-TNX (RCCX) modules in the major histocompatibility complex. Am J Hum Genet 2002; 71: 823–837.

    Article  Google Scholar 

  20. Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J et al. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60: 1–18.

    Article  CAS  Google Scholar 

  21. Wu YL, Yang Y, Chung EK, Zhou B, Kitzmiller KJ, Savelli SL et al. Phenotypes, genotypes and disease susceptibility associated with gene copy number variations: complement C4 CNVs in European American healthy subjects and those with systemic lupus erythematosus. Cytogenet Genome Res 2008; 123: 131–141.

    Article  CAS  Google Scholar 

  22. Lee HH . Diversity of the CYP21P-like gene in CYP21 deficiency. DNA Cell Biol 2005; 24: 1–9.

    Article  Google Scholar 

  23. Lee HH, Tsai FJ, Lee YJ, Yang YC . Diversity of the CYP21A2 gene: a 6.2-kb TaqI fragment and a 3.2-kb TaqI fragment mistaken as CYP21A1P. Mol Genet Metab 2006; 88: 372–377.

    Article  CAS  Google Scholar 

  24. Koppens PF, Hoogenboezem T, Degenhart HJ . Duplication of the CYP21A2 gene complicates mutation analysis of steroid 21-hydroxylase deficiency: characteristics of three unusual haplotypes. Hum Genet 2002; 111: 405–410.

    Article  CAS  Google Scholar 

  25. Wu YL, Savelli SL, Yang Y, Zhou B, Rovin BH, Birmingham DJ et al. Sensitive and specific real-time polymerase chain reaction assays to accurately determine copy number variations (CNVs) of human complement C4A, C4B, C4-long, C4-short, and RCCX modules: elucidation of C4 CNVs in 50 consanguineous subjects with defined HLA genotypes. J Immunol 2007; 179: 3012–3025.

    Article  CAS  Google Scholar 

  26. Laki J, Kiszel P, Vatay A, Blasko B, Kovacs M, Korner A et al. The HLA 8.1 ancestral haplotype is strongly linked to the C allele of -429 T>C promoter polymorphism of receptor of the advanced glycation endproduct (RAGE) gene. Haplotype-independent association of the -429C allele with high hemoglobinA1C levels in diabetic patients. Mol Immunol 2007; 44: 648–655.

    Article  CAS  Google Scholar 

  27. Vatay A, Yang Y, Chung EK, Zhou B, Blanchong CA, Kovacs M et al. Relationship between complement components C4A and C4B diversities and two TNFA promoter polymorphisms in two healthy Caucasian populations. Hum Immunol 2003; 64: 543–552.

    Article  CAS  Google Scholar 

  28. Baumgartner-Parzer SM, Fischer G, Vierhapper H . Predisposition for de novo gene aberrations in the offspring of mothers with a duplicated CYP21A2 gene. J Clin Endocrinol Metab 2007; 92: 1164–1167.

    Article  CAS  Google Scholar 

  29. Aly TA, Eller E, Ide A, Gowan K, Babu SR, Erlich HA et al. Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 2006; 55: 1265–1269.

    Article  CAS  Google Scholar 

  30. Candore G, Campagna AM, Cuppari I, Di Carlo D, Mineo C, Caruso C . Genetic control of immune response in carriers of the 8.1 ancestral haplotype: correlation with levels of IgG subclasses: its relevance in the pathogenesis of autoimmune diseases. Ann N Y Acad Sci 2007; 1110: 151–158.

    Article  CAS  Google Scholar 

  31. Corvol H, Beucher J, Boelle PY, Busson PF, Muselet-Charlier C, Clement A et al. Ancestral haplotype 8.1 and lung disease severity in European cystic fibrosis patients. J Cyst Fibros 2012; 11: 63–67.

    Article  Google Scholar 

  32. Rojana-udomsart A, Needham M, Luo YB, Fabian V, Walters S, Zilko PJ et al. The association of sporadic inclusion body myositis and Sjogren's syndrome in carriers of HLA-DR3 and the 8.1 MHC ancestral haplotype. Clin Neurol Neurosurg 2011; 113: 559–563.

    Article  CAS  Google Scholar 

  33. Abdou AM, Gao X, Cozen W, Cerhan JR, Rothman N, Martin MP et al. Human leukocyte antigen (HLA) A1-B8-DR3 (8.1) haplotype, tumor necrosis factor (TNF) G-308 A, and risk of non-Hodgkin lymphoma. Leukemia 2010; 24: 1055–1058.

    Article  CAS  Google Scholar 

  34. Mohammadi J, Ramanujam R, Jarefors S, Rezaei N, Aghamohammadi A, Gregersen PK et al. IgA deficiency and the MHC: assessment of relative risk and microheterogeneity within the HLA A1 B8, DR3 (8.1) haplotype. J Clin Immunol 2010; 30: 138–143.

    Article  CAS  Google Scholar 

  35. Mao R, McDonald J, Cantwell M, Tang W, Ward K . The implication of de novo 21-hydroxylase mutation in clinical and prenatal molecular diagnoses. Genet Test 2005; 9: 121–125.

    Article  CAS  Google Scholar 

  36. Muers M . Complex disease: ups and downs at the MHC. Nat Rev Genet 2011; 12: 456–457.

    Article  CAS  Google Scholar 

  37. Traherne JA . Human MHC architecture and evolution: implications for disease association studies. Int J Immunogenet 2008; 35: 179–192.

    Article  CAS  Google Scholar 

  38. Zweers MC, Bristow J, Steijlen PM, Dean WB, Hamel BC, Otero M et al. Haploinsufficiency of TNXB is associated with hypermobility type of Ehlers-Danlos syndrome. Am J Hum Genet 2003; 73: 214–217.

    Article  CAS  Google Scholar 

  39. Odell D, Maciulis A, Cutler A, Warren L, McMahon WM, Coon H et al. Confirmation of the association of the C4B null allelle in autism. Hum Immunol 2005; 66: 140–145.

    Article  CAS  Google Scholar 

  40. Mayilyan KR, Dodds AW, Boyajyan AS, Soghoyan AF, Sim RB . Complement C4B protein in schizophrenia. World J Biol Psychiatry 2008; 9: 225–230.

    Article  Google Scholar 

  41. Zafar GI, Grimm EA, Wei W, Johnson MM, Ellerhorst JA . Genetic deficiency of complement isoforms C4A or C4B predicts improved survival of metastatic renal cell carcinoma. J Urol 2009; 181: 1028–1034 ; discussion 34.

    Article  CAS  Google Scholar 

  42. Szilagyi A, Blasko B, Szilassy D, Fust G, Sasvari-Szekely M, Ronai Z . Real-time PCR quantification of human complement C4A and C4B genes. BMC Genet 2006; 7: 1.

    Article  Google Scholar 

  43. Excoffier L, Laval G, Schneider S . Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 2005; 1: 47–50.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Research Foundation (OTKA-NKTH 80842 (GF)). We thank Dr Zoltán Prohászka for his valuable comments and suggestions on this work.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Á Szilágyi.

Ethics declarations

Competing interests

The authors declare no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bánlaki, Z., Doleschall, M., Rajczy, K. et al. Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes. Genes Immun 13, 530–535 (2012). https://doi.org/10.1038/gene.2012.29

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/gene.2012.29

Keywords

Search

Quick links