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Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters

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Abstract

Genome analysis of the swine leukocyte antigen (SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen (HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.

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Acknowledgements

We would like to thank Dr. Yasunari Matsuzaka, Akihiro Denda, and Gen Tamiya, for helpful information regarding the human novel genes surrounding the CDSN gene. We also wish to thank Dr. Tetsushi Yamagata and Tatsuya Anzai for useful discussion. This study was supported by grants from the Ministry of Education, Sports, Science, Culture and Technology, Japan, and the Animal Genome Research Project of the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Authors and Affiliations

  1. Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Isehara, 259-1193, Kanagawa, Japan

    Atsuko Shigenari, Asako Ando, Takashi Shiina, Jerzy K. Kulski & Hidetoshi Inoko

  2. Laboratoire de Radiobiologie et d’Etude du Genome, INRA-CEA, Jouy-en-Josas, France

    Christine Renard & Patrick Chardon

  3. Centre for Bioinformatics and Biological Computing, School of Information Technology, Division of Arts, Murdoch University, 6150, Murdoch, Western Australia, Australia

    Jerzy K. Kulski

  4. Genome Research Department, National Institute of Agrobiological Sciences, Ibaraki, Japan

    Hiroshi Yasue

Authors
  1. Atsuko Shigenari
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  2. Asako Ando
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  3. Christine Renard
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  4. Patrick Chardon
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  5. Takashi Shiina
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  6. Jerzy K. Kulski
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  7. Hiroshi Yasue
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  8. Hidetoshi Inoko
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Corresponding author

Correspondence to Hidetoshi Inoko.

Additional information

The nucleotide sequence data reported in this paper have been submitted to DDBJ, EMBL and GenBank databases under accession numbers AB113354, AB113355, AB113356, AB113357

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Shigenari, A., Ando, A., Renard, C. et al. Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters. Immunogenetics 55, 695–705 (2004). https://doi.org/10.1007/s00251-003-0627-0

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  • DOI: https://doi.org/10.1007/s00251-003-0627-0

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