Summary
We have analysed continuous genomic sequence of 1.8 Mb from the HLA class I region of the MHC with a view to understanding the evolution, organisation and sequential interrelationships between members of the multicopy HLA class I and PERB11 (MIC) gene families, human endogenous retroviruses (HERVs) and retroelements that are distributed within this region. Analysis and mapping of genomic sequence from PERB 11.2 (MICB) to HLA-F has revealed that the multicopy HLA and PERB11 (MIC) sequences, HERV-16 (P5 gene family) and associated retroelements such as Alu, LTR, MER and LI are contained within repeated segments that can be classified into at least 6 groups based on the distinctive features of paralogous transposable elements. Most of these segments appear to have evolved from a basic duplication unit or duplicon composed of a HLA class I, HERV-16 (P5) and PERB II (MIC) sequence, and the associated retroelements. Exponential amplification of duplicons by diversifying single and multisegmental duplications has resulted in many copies of pseudogenes and gene fragments, and three subgenomic blocks (alpha, beta, and kappa) that differ in the number, orientation and complexity of duplicons. Retroelements, particularly HERV-16, are closely associated with the breakpoints within and between duplicons (Kulski et al 1999b), suggesting that they have had a major role in the spread and diversity of the multicopy gene families.
From our analyses we conclude that the HLA class I genomic region is a metameric design of three distinct subgenomic blocks that are characterised by the presence of HLA class I, HERV-16 and PERB11 (MIC) sequences and distinctive retroelements. The blocks have evolved metamerismatically by the expansion and contraction of duplicons involving retroelements and basic recombination processes such as duplications, insertions, deletions and translocations. In this context, we also consider the distribution of many transposable elements within the MHC as “bandaids’ or “scars” brought about in response to genomic stress or damage.
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References
Abi Rached L, McDermott MF, Pontarotti P (1999) The MI-IC big bang. Immunol Rev 167: 33–45
Abraham Li, Leelayuwat C, Grimsley G, Degli-Esposti MA, Mann A, Zhang WJ, Christiansen FT, Dawkins RL (1992) Sequence differences between HLA-B and TNF distinguish different MHC ancestral haplotypes. Tissue Antigens 39: 117–121
Andersson G, Svensson AC, Setterblad N, Rask L (1998) Retroelements in the human MHC class II region. Trends Genet 14: 109–114
Bahram S, Bresnahan M, Geraghty DE, Spies T (1994) A second lineage of mammalian major histocompatibility complex class I genes. Proc Natl Acad Sci USA 91: 6259–6263
Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E (1996) Standardized nomenclature for Alu repeats. J Mol Evol 42: 3–6
Beck S, Abdulla S, Alderton RP, Glynne RJ, Gut IG, Hosking LK, Jackson A, Kelly A, Newell WR, Sanseau P, Radley E, Thorpe KL, Trowsdale J (1996) Evolutionary dynamics of non-coding sequences within the class II region of the human MHC. J Mol Biol 255: 1–13
Boeke JD (1997) LINEs and Alus-the polyA connection. Nat Genet 16: 6–7
Chu W-M, Ballard R, Carpick BW, Williams BRG, Schmid CW (1998) Potential Alufunction: Regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 18: 58–68
Dawkins R, Leelayuwat C, Gaudieri S, Tay G, Hui J, Cattley S, Martinez P, Kulski J (1999) Genomics of the Major Histocompatibility Complex: Haplotypes, retroviruses and disease. Immunol Rev 167: 275–304
El Kahloun A, Vernet C, Jouanolle A-M, Boretto J, Mauvieux V, LeGall J-Y, David V, Pontarotti P (1992) A continuous restriction map from FILA-E to HLA-F. Structural comparison between different HLA-A haplotypes. Immunogenetics 35: 183–189
El Kahloun A, Chauvel B, Mauvieux V, Dorval I, Jouanolle A-M, Gicquel I, Le Gall J-Y, David V (1993) Localization of seven new genes around the HLA-A locus. Hum Mol Genet 2: 55–60
Gaudieri S, Giles K, Kulski J, Dawkins R (1997a) Duplication and polymorphism in the MHC: Alu generated diversity and polymorphism within the PERB11 gene family. Hereditas 127: 37–46
Gaudieri S, Kulski JK, Balmer L, Giles KM, Inoko H, Dawkins RL (1997b) Retroelements and segmental duplications in the generation of diversity within the MHC. DNA Seq 8: 137–141
Gaudieri S, Kulski JK, Dawkins RL, Gojobori (1999) Different evolutionary histories in two subgenomic regions of the Major Histocompatibility Complex. Genome Res 9: 541–549
Geraghty DE, Koller BH, Hansen JA, Orr HT (1992) The FILA class I gene family includes at least six genes and twelve pseudogenes and gene fragments. J Immunol 149: 1934–1946
Gould SJ (1989) Wonderful Life. The Burgess Shale and the Nature of History. Penguin Books LTD, London, England
Grimsley C, Mather KA, Ober C (1998) HLA-H: a pseudogene with increased variation due to balancing selection at neighboring loci. Mol Biol Evol 15: 1581–1588
Groh V, Steinle A, Bauer S, Spies T (1998) Recognition of stress-induced MHC molecules by intestinal epithelial gamma delta T cells. Science 279: 1737–1740
Hoegstrand K, Boehme J (1999) Gene conversion can create new MHC alleles. Immunol Rev 167: 305–317
Hughes AL (1995) Origin and evolution of FILA class I pseudogenes. Mol Biol Evol 12: 247–258
Jurka J, Klonowski P, Dagman V, Pelton P (1996b) CENSOR- a program for identification and elimination of repetitive elements from DNA sequences. Comp Chem 20: 119–121
Kapitonov V, Jurka J (1996) The age of Alu subfamilies. J Mol Evol 42: 59–65
Kazazian HH, Moran JV (1998) The impact of LI retrotransposons on the human genome. Nat Genet 19: 19–24
Klein J, Sato A, O’hUigin C (1998) Evolution by gene duplication in the major histocompatibility complex. Cytogenet Cell Genet 80: 123–127
Klein J, Zhu Z, Gutknecht J, Figueroa F, Kasahara M (1991) Lessons in evolution. In: Srivastava R, Ram BP, Tyle P (eds) Immunogenetics of the Major Histocompatibility Complex. VCH, New York, pp 18–38
Komatsu-Wakui M, Tokunaga K, Ishikawa Y, Kashiwase K, Moriyama S, Tsuchiya N, Ando H, Shiina T, Geraghty DE, Inoko H, Juji T (1999) MIC-A polymorphism in Japanese and a MIC-A-MIC-B null haplotype. Immunogenetics 49: 620–628
Kornberg A (1980) DNA Replication. WH Freeman and Co., New York
Kulski JK, Dawkins RL (1999) The P5 multicopy gene family in the MHC is related in sequence to human endogenous retroviruses HERV-L and HERV-16. Immunogenetics 49: 404–412
Kulski JK, Gaudieri S, Bellgard M, Balmer L, Giles K, Inoko H, Dawkins RL (1997) The evolution of MHC diversity by segmental duplication and transposition of retroelements. J Mol Evol 45: 599–609
Kulski JK, Gaudieri S, Inoko T, Dawkins RL (1999a) Comparison between two HERVrich regions within the Major Histocompatibility Complex. J Mol Evol 48: 675–683
Kulski JK, Gaudieri S, Martin A, Dawkins RL (1999b) Coevolution of PERB l 1 (MIC) and FILA class I genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol 49: 84–97
Lania L, Di Cristofano A, Strazzullo M, Majello B, La Mantia G (1992) Structural and functional organization of the human endogenous retroviral ERV9 sequences. Virology 191.464–468
Leelayuwat C, Townsend DC, Degli-Esposti MA, Abraham LJ, Dawkins RL (1994) A new polymorphic and multicopy MHC gene family related to non-mammalian class I. Immunogenetics 40: 339–351
Leelayuwat C, Pinelli M, Dawkins RL (1995) Clustering of diverse replicated sequences in the MHC. Evidence for en bloc duplication. J Immunol 155: 692–698
Marshall B, Leelayuwat C, Degli-Eposti MA, Pinelli M, Abraham LI, Dawkins RL (1993) New major histocompatibility complex genes. Hum Immunol 38: 24–29
Martin RD (1993) Primate origins: plugging the gaps. Nature 363: 223–234
Maueler W, Kyas A, Keyl H-G, Epplen J (1998) A genome-derived (gaa.ttc)24 trinucleotide block binds nuclear protein(s) specifically and forms triple helices. Gene 215: 389–403
McClintock B (1984) The significance of responses of the genome to challenge. Science 226: 792–801
Miki Y (1998) Retrotransposal integration of mobile genetic elements in human diseases. J Hum Genet 43: 77–84
Mizuki N, Ando H, Kimura M, Ohno S, Miyata S, Yamazaki M, Tashiro H, Watanabe K, Ono A, Taguchi S, Sugawara C, Fukuzumi Y, Okumura K, Goto K, Ishihara M, Nakamura S, Yonemoto J, Kikuti YY, Shiina T, Chen L, et al. (1997) Nucleotide sequence analysis of the HLA class I region spanning the 237-kb segment around the HLA-B and -C genes. Genomics 42: 55–66
Nei M, Gu X, Sitnikova T (1997) Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci USA 94: 7799–7806
Nouvel P (1994) The mammalian genome shaping activity of reverse transcriptase. Genetica 93: 191–201
Parham P, Lomen CE, Lawlor DA, Ways JP, Holmes N, Coppin HL, Salter RD, Wan AM, Ennis PD (1988) Nature of polymorphism in HLA-A, -B, and -C molecules. Proc Natl Acad Sci USA 85: 4005–4009
Pichon L, Cam G, Bouric P, Giffon T, Chauvel B, Lepourcelet M, Mosser J, Legall J-V, David V (1996) Structural analysis of the I-ILA-A/HLA-F subregion: precise localization of two new multigene families closely associated with the HLA class I sequences. Genomics 32: 236–244
Santos EJM, Epplen JT, Epplen C, Guerreiro JF (1998) Microsatellite evolution in the 5’UTR of the HLA-F gene. Human Evol 13: 57–64
Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas, TP, DeBerardinis RJ, Gabriel A, Swegold GD, Kazazian Jr FIH (1997) Many human LI elements are capable of retrotransposition. Nat Genet 16: 37–43
Satta Y, Li YJ, Takahata N (1998) The neutral theory and natural selection in the HLA region. Front Biosci 27: d459–467
Schmid CW (1996) Alu structure, origin, evolution, significance, and function of one-tenth of human DNA. Prog Nucleic Acids Res Mol Biol 53: 283–319
Shiina T, Tamiya G, Oka A, Takishima N, Inoko H (1999) Genome sequence analysis of the 1.8 Mb entire human MHC class I region. Immunol Rev 176: 193–199
Shiina T, Tamiya A, Oka A, Yamagata T, Yamagata N, Kikkawa E, Goto A, Mizuki N, Watanabe K, Fukuzumi Y, Taguchi S, Sugawara C, Ono A, Chen L, Yamazaki M, Tashiro H, Ando A, Ikemura T, Kimura M, Inoko H (1998) Nucleotide sequencing analysis of the 146-kilobase segment around the IkBL and MICA genes at the centromeric end of the HLA Class I region. Genomics 47: 372–382
Smit AFA (1996) The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6: 743–748
Smit AFA, Toth G, Riggs AD, Jurka J (1995) Ancestral, mammalian-wide subfamilies of LINE-I repetitive sequences. J Mol Biol 246: 401–417
Soyfer VN, Potaman VN (1996) Triple-helical Nucleic Acids. Springer-Verlag, New York
Teng S-C, Kim B, Gabriel A (1996) Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383: 641–644
Venditti CP, Chomey MJ (1992) Class I gene contraction within the HLA-A subregion of the human MHC. Genomics 14: 1003–1009
Venditti CP, Harris JM, Geraghty DE, Chomey MJ (1994) Mapping and characterization of non-HLA multigene assemblages in the human MHC class I region. Genomics 22: 257–266
Vernet C, Ribouchon MT, Chimini G, Jouanolle AM, Sidibe I, Pontarotti P (1993) A novel coding sequence belonging to a new multicopy gene family mapping within the human MHC class I region. Immunogenetics 38: 47–53
Watanabe Y, Tokunaga K, Geraghty DE, Tadokoro K, Juji T (1997) Large-scale comparative mapping of the MHC class I region of predominant haplotypes in Japanese. Immunogenetics 46: 135–141
Yamazaki M, Tateno Y, Inoko H (1999) Genomic organisation around the centromeric end of the HLA class I region: large-scale sequence analysis. J Mol Evol 48: 317–327
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Kulski, J.K., Gaudieri, S., Dawkins, R.L. (2000). Transposable elements and the metamerismatic evolution of the HLA class I region. In: Kasahara, M. (eds) Major Histocompatibility Complex. Springer, Tokyo. https://doi.org/10.1007/978-4-431-65868-9_11
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DOI: https://doi.org/10.1007/978-4-431-65868-9_11
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