Browse > Article
http://dx.doi.org/10.5187/JAST.2007.49.5.549

cSNP Identification and Genotyping from C4B and BAT2 Assigned to the SLA Class III Region  

Kim, J.H. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
Lim, H.T. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
Seo, B.Y. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
Lee, S.H. (Gyeongnam animal science and technology, Gyeongsang National University)
Lee, J.B. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
Yoo, C.K. (Division of Agriculture and Life, Gyeongsang National University)
Jung, E.J. (Division of Agriculture and Life, Gyeongsang National University)
Jeon, J.T. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
Publication Information
Journal of Animal Science and Technology / v.49, no.5, 2007 , pp. 549-558 More about this Journal
Abstract
C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.
Keywords
C4B; BAT2; cSNP; Multiplex-ARMS; Direct sequencing; Genotyping; SLA;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Blasko, B., Szeplaki, G., Varge, L., Ronai, Z., Prohaszka, Z., Sasvari-Szekely, M., Visy, B., Farkas, H. and Fust, G. 2007. Relationship between copy number of genes (C4A, C4B) encoding the fourth component of complement and the clinical course of hereditary angioedema (HAE). Mol. Immunol. 44:2667-2674   DOI   ScienceOn
2 Balbi, G., Ferrera, F., Rizzi, M., Piccioli, P., Morabito, A., Cardamone, L., Ghio, M., Palmosano, G. L., Carrara, P., Pedemonte, S., Sessarego, M., De Angioletti, M., Notaro, R., Indiveri, F. and Pistillo, M. P. 2007. Association of -318 C/T and +49 A/G cytotoxic T lymphocyte antigen-4 (CTLA-4) gene polymorphisms with a clinical subset of Italian patients with systemic sclerosis. Clin. Exp. Immunol. 149:40-47   DOI   ScienceOn
3 Cascalho, M. and Platt, J. L. 2001. The Immunological barrier to xenotransplantation. Immunity 14:437-446   DOI   ScienceOn
4 Chen, F., Xie, J., Xhou, Y., Li, N. and Chou, K. Y. 2004. Novel SLA-DR alleles of three Chinese pig strains and the related function in human T cell response, Cell. Mol. Immunol. 1:212-21
5 Geffrotin, C., Popescu, C. P., Cribiu, E. P., Boscher, J., Renard, C., Chardon, P. and Vaiman, M. 1984. Assignment of MHC in swine to chromosome 7 by in situ hybridization and serological typing. Ann. Genet. 27-213-219
6 Ittiprasert, W., Kantachuvesiri, S., Pavasuthipaisit, K., Verasertniyom, O., Chaomthum, L., Totemchokchyakam, K. and Kitiyanant, Y. 2005. Complete deficiencies of complement C4A and C4B including 2-bp insertion in codon 1213 are genetiv risk factors of systemic lupus erythemaotosus in thai populations. J. Autoimmune. 25:77-9-84   DOI   ScienceOn
7 Lacerra, G., Musollino, G., Di Noce, F., Prezioso, R. and Carestia, C. 2007. Genotyping for known Mediterranean alpha-thalassemia point mutations using a multiplex amplification refractory mutation system. Haematologica. 92:254-255   DOI
8 Lee, J. H., Simond, D., Hawthorne, W. J., Walters, S. N., Patel, A. T., Smith, D. M., O'Connell, P. J. and Moran, C. 2005. Characterization of the swme major histocompatibility complex alleles at eight loci in Westran pigs. Xenotransplantation 12:303-307   DOI   ScienceOn
9 Martens, G. W., Lunney, J. K., Baker, J. E. and Smith, D. M. 2003. Rapid assignment of swine leukocyte antigen haplotypes in pedigreed herds using a polymerase chain reaction-based assay. Immunogenetics 55:395-401   DOI
10 Banerji, J., Sands, J., Strominger, J. L. and Spies, T. 1990. A gene pair from the human major histocompatibility complex encodes large prolinerich proteins with multiple repeated motifs and a single ubiquitin-like domain. Proc. Nat. Acad. Sci. 87:2374-2378
11 Sachs, D. H., Leight, G., Cone, J., Schwarz, S., Stuart, L. and Rosenberg, S. 1976. Transplantation in miniature swine. I. Fixation of the major histocompatibility complex. Transplantation. 22:559-567   DOI
12 Schroeder, H. W., Zhu, Z. B., March, R. E., Campbell, R. D., Berney, S. M., Nedospasov, S. A., Turetskaya, R. L., Atkinson, T. P., Go, R. C., Cooper, M. D. and Volanakis, J. E. 1998. Susceptibility locus for IgA deficiency and common variable immunodeficiency in the HLA-DR3-B8-A1 haplotype. Mol. Med. 4:72-86
13 Shichi, D., Kikkawa, E. F., Ota, M., Katsuyama, Y., Kimura, A., Matsumori, A., Kulski, J. K., Naruse, T. K. and Inoko, H. 2005. The haplotype block, NFKBIL1-ATP6V1G2-BAT1-MICB-MICA, within the class III class I boundary region of the human major histocompatibility complex may control susceptibility to hepatitis C virus-associated dilated cardiomyopathy. Tissue Antigens 66:200-208   DOI   ScienceOn
14 Smith, D. M., Lunney, J. K., Martens, G. W., Ando, A., Lee, J. H., Ho, C. S., Schook, L., Renard, C. and Chardon, P. 2005. Nomenclature for factors of the SLA class-I system, 2004. Tissue Antigens 65:136-149   DOI   ScienceOn
15 Hashimoto, M., Nakamura, N., Obayashi, H., Kimura, F., Moriwaki., A., Hasegawa, G., Shigeta, H., Kitagawa, Y., Nakano, K., Kondo, M., Ohta, M. and Nishimura, M. 1999. Genetic constributation of the BAT2 gene microsatellite polymorphism to the age-at-onset of insulin-dependent diabetes mellitus. Hum. Genet. 105:197-199   DOI
16 Rothbard, J. B. and Gefter, M. L. 1991. Interactions between immunogenic peptides and MHC proteins. Annu. Rev. Immunol. 9:527-565   DOI   ScienceOn
17 Ierino, F. L., Gojo, S., Banerjee, P. T., Giovino, M., Xu, Y., Gere, J., Kaynor, C., Awwad, M., Monroy, R., Rembert, J., Hatch, T., Foley, A., Kozlowski, T., Yamada, K., Neethling, F. A., Fishman, J., Bailin, M., Spitzer, T. R., Cooper, D. K., Cosimi, A. B., LeGeurn, C. and Sachs, D. H. 1999. Transfer of swine major histocompatibility complex class II genes into autologous bone marrow cells of baboons for the induction of tolerance across xenogeneic barriers. Transplantation. 67:1119-1128   DOI   ScienceOn
18 Okamoto, K., Makino, S., Yoshikawa, Y., Takaki, A., Nagatsuka, Y., Ota, M., Tamiya, G., Kimura, A., Bahram, S. and Inoko, H. 2003. Identification of IkBL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am. J. Hum. Genet. 72:303-312   DOI   ScienceOn
19 Chardon, P., Renard, C. and Vaiman, M. 1999. The major hostocompatibility complex in swine. Immunol. Rev. 167:179-192   DOI   ScienceOn
20 Martinez, A., Salido, M., Bonilla, G., PascualSalcedo, D., Femandez-Arquero, M., de Miguel, S., Balsa, A., de la Concha, E. G. and Ferrtandez-Gutierrez, B. 2004. Association of the major histocompatibility complex with response to infliximab therapy in rheumatoid arthritis patients. Arthritis Rheum. 50:1077-1082   DOI   ScienceOn
21 O'Connell, P. J., Hawthorne, W. J., Simond, D., Chapman, J. R., Chen, Y., Patel, A. T., Welters, S. N., Burgess, J., Weston, L., Stokes, R. A., Moran, C. and Allen, R. 2005. Genetic and functional evaluation of the level of inbreeding of the Westran pig; a herd with potential for use in xenotransplantation. Xenotransplantation. 12:308-315   DOI   ScienceOn
22 Taylor, A., Tabrah, S., Wang, D., Sozen, M., Duxbury, M., Whittall, R, Humphries, S. E. and Norbury, G. 2007. Multiplex ARMS analysis to detect 13 common mutations in familial hypercholesterolaemia. Clin. Genet. 71:561-568   DOI   ScienceOn
23 Renard, C., Hart, E., Sehra, H., Beasley, H., Coggill, P., Howe, K., Harrow, J., Gilbert, J., Sims, S., Rogers, J., Ando, A., Shigenari, A., Shiina, T., Inoko, H., Chardon, P. and Beck, S. 2006. The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 88:96-110   DOI   ScienceOn
24 Robins, T., Bellanne-Chantelot, C., Barbaro, M., Cabrol, S., Wedell, A. and Lajic, S. 2007. Characterization of novel missense mutation in CYP21 causing congenital adrenal hyperplasia. J. Mol. Med. 85:247-255   DOI
25 Sachs, D. H. 1994. The pig as a potential xenograft donor. pathol. Biol. 42:185-191
26 Tsuda, T., Moriguchi, M., Asanuma, Y., Imamura, S., Toyoda, A., Yamada, S., Terai, C., Suzuki, K. and Tabei, K. 2007. C4B deficiency association with membranoproliferative glomerulonephritis. Intem. Med. 46:756-770
27 Yang, Y., Lhotta, K., Chung, E. K., Eder, P., Neumair, F. and Yu, C. Y. 2004. Complete complement components C4A and C4B deficiencies in juman kidney diseases and systemiclupus erythematosus. J. Immunol. 173:2803-2814   DOI
28 Wu, Q., Xiong, P., Liu, J. Y., Feng, S. T., Gong, F. L. and Chen, S. 2004. The study of new SLA classical molecules in inbreeding Chinese Wuzhishan pig. Transplant. P. 36:2483-2484
29 Xie, T., Rowen, L., Aguado, B., Ahearn, M. E., Madan, A., Qin, S., Campbell, R. D. and Hool. L. 2003. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res. 13:2621-2626   DOI   ScienceOn