Gene map of the extended human MHC (original) (raw)
Gorer, P. A. The detection of a hereditary antigenic difference in the blood of mice by means of human group A serum. J. Genet.32, 17–31 (1936). Article Google Scholar
Klein, J. Seeds of time: fifty years ago Peter A. Gorer discovered the H-2 complex. Immunogenetics24, 331–338 (1986). ArticleCASPubMed Google Scholar
Klein, J. Natural History of the Major Histocompatibility Complex (Wiley & Sons, New York, 1986). Google Scholar
The MHC sequencing consortium. Complete sequence and gene map of a human major histocompatibility complex.Nature401, 921–923 (1999). Describes the first sequence-based gene map of a (mosaic) human MHC.
Malfroy, L. et al. Heterogeneity in rates of recombination in the 6-Mb region telomeric to the human major histocompatibility complex. Genomics43, 226–231 (1997). This paper describes the first evidence (linkage disequilibrium) for the existence of an extended MHC. ArticleCASPubMed Google Scholar
Yoshino, M. et al. Genomic evolution of the distal Mhc class I region on mouse Chr 17. Hereditas127, 141–148 (1997). ArticleCASPubMed Google Scholar
Stephens, R. et al. Gene organisation, sequence variation and isochore structure at the centromeric boundary of the human MHC. J. Mol. Biol.291, 789–799 (1999). ArticleCASPubMed Google Scholar
Mungall, A. J. et al. The DNA sequence and analysis of human chromosome 6. Nature425, 805–811 (2003). ArticleCASPubMed Google Scholar
Stewart, C. A. et al. Complete MHC haplotype sequencing for common disease gene mapping. Genome Res.14, 1176–1187 (2004). The authors describe the sequences in the MHC from single haplotypes. ArticleCASPubMedPubMed Central Google Scholar
Kumanovics, A., Takada, T. & Lindahl, K. F. Genomic organization of the mammalian MHC. Annu. Rev. Immunol.21, 629–657 (2003). ArticleCASPubMed Google Scholar
Freemont, P. S., Hanson, I. M. & Trowsdale, J. A novel cysteine-rich sequence motif. Cell64, 483–484 (1991). ArticleCASPubMed Google Scholar
Wain, H. M., Lush, M. J., Ducluzeau, F., Khodiyar, V. K. & Povey, S. Genew: the human gene nomenclature database, 2004 updates. Nucleic Acids Res.32, D255–257 (2004). ArticleCASPubMedPubMed Central Google Scholar
Robinson, J. et al. IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.Nucleic Acids Res.31, 311–314 (2003). ArticleCASPubMedPubMed Central Google Scholar
Ehlers, A. et al. MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes. Genome Res.10, 1968–1978 (2000). ArticleCASPubMedPubMed Central Google Scholar
Xie, T. et al. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res.13, 2621–2636 (2003). ArticleCASPubMedPubMed Central Google Scholar
Eddy, S. R. Non-coding RNA genes and the modern RNA world. Nature Rev. Genet.2, 919–929 (2001). ArticleCASPubMed Google Scholar
Yang, Z., Mendoza, A. R., Welch, T. R., Zipf, W. B. & Yu, C. Y. Modular variations of the human major histocompatibility complex class III genes for serine/threonine kinase RP, complement component C4, steroid 21-hydroxylase CYP21, and tenascin TNX (the RCCX module). A mechanism for gene deletions and disease associations. J. Biol. Chem.274, 12147–12156 (1999). ArticleCASPubMed Google Scholar
Bergstrom, T. F. et al. Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences.Immunol. Rev.167, 351–365 (1999). ArticleCASPubMed Google Scholar
Kulski, J. K. & Dawkins, R. L. The P5 multicopy gene family in the MHC is related in sequence to human endogenous retroviruses HERV-L and HERV-16. Immunogenetics49, 404–412 (1999). ArticleCASPubMed Google Scholar
Bailey, J. A. et al. Recent segmental duplications in the human genome. Science297, 1003–1007 (2002).This paper shows that duplication is a common feature of the human genome and that it is not restricted to known (for example, immune) multigene families. ArticleCASPubMed Google Scholar
Gu, X., Wang, Y. & Gu, J. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genet.31, 205–209 (2002). ArticleCASPubMed Google Scholar
Trowsdale, J. The gentle art of gene arrangement: the meaning of gene clusters. Genome Biol.3, COMMENT2002 (2002).
Marzluff, W. F., Gongidi, P., Woods, K. R., Jin, J. & Maltais, L. J. The human and mouse replication-dependent histone genes. Genomics80, 487–498 (2002). ArticleCASPubMed Google Scholar
Zhang, E. Y., Knipp, G. T., Ekins, S. & Swaan, P. W. Structural biology and function of solute transporters: implications for identifying and designing substrates. Drug Metab. Rev.34, 709–750 (2002). ArticleCASPubMed Google Scholar
Ruddy, D. A. et al. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. Genome Res.7, 441–456 (1997). ArticleCASPubMed Google Scholar
Shibui, A. et al. Isolation and chromosomal mapping of a novel human gene showing homology to Na+/PO4 cotransporter.J. Hum. Genet.44, 190–192 (1999). ArticleCASPubMed Google Scholar
Radosavljevic, M. & Bahram, S. In vivo immunogenetics: from_MIC_ to RAET1 loci. Immunogenetics55, 1–9 (2003). ArticleCASPubMed Google Scholar
Bahram, S. _MIC_genes: from genetics to biology. Adv. Immunol.76, 1–60 (2000). CASPubMed Google Scholar
Hopper, A. K. & Phizicky, E. M. tRNA transfers to the limelight. Genes Dev.17, 162–180 (2003). ArticleCASPubMed Google Scholar
Buckland, R. A., Maule, J. C. & Sealey, P. G. A cluster of transfer RNA genes (TRM1, TRR3, and TRAN) on the short arm of human chromosome 6. Genomics35, 164–171 (1996). ArticleCASPubMed Google Scholar
Rhodes, D. A., Stammers, M., Malcherek, G., Beck, S. & Trowsdale, J. The cluster of BTN genes in the extended major histocompatibility complex. Genomics71, 351–362 (2001). ArticleCASPubMed Google Scholar
Stammers, M., Rowen, L., Rhodes, D., Trowsdale, J. & Beck, S. BTL-II: a polymorphic locus with homology to the butyrophilin gene family, located at the border of the major histocompatibility complex class II and class III regions in human and mouse. Immunogenetics51, 373–382 (2000). ArticleCASPubMed Google Scholar
Jack, L. J. & Mather, I. H. Cloning and analysis of cDNA encoding bovine butyrophilin, an apical glycoprotein expressed in mammary tissue and secreted in association with the milk-fat globule membrane during lactation.J. Biol. Chem.265, 14481–14486 (1990). ArticleCASPubMed Google Scholar
Giorgi, D., Friedman, C., Trask, B. J. & Rouquier, S. Characterization of nonfunctional V1R-like pheromone receptor sequences in human. Genome Res.10, 1979–1985 (2000). ArticleCASPubMedPubMed Central Google Scholar
Volz, A. et al. Complex transcription and splicing of odorant receptor genes. J. Biol. Chem.278, 19691–19701 (2003). ArticleCASPubMed Google Scholar
Ziegler, A., Dohr, G. & Uchanska-Ziegler, B. Possible roles for products of polymorphic MHC and linked olfactory receptor genes during selection processes in reproduction. Am. J. Reprod. Immunol.48, 34–42 (2002). ArticlePubMed Google Scholar
Coleman, J. E. Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins.Annu. Rev. Biochem.61, 897–946 (1992). ArticleCASPubMed Google Scholar
Lee, P. L. et al. Three genes encoding zinc finger proteins on human chromosome 6p21.3: members of a new subclass of the Kruppel gene family containing the conserved SCAN box domain. Genomics43, 191–201 (1997). ArticleCASPubMed Google Scholar
Meyer, M., Gaudieri, S., Rhodes, D. A. & Trowsdale, J. Cluster of _TRIM_genes in the human MHC class I region sharing the B30.2 domain.Tissue Antigens61, 63–71 (2003). ArticleCASPubMed Google Scholar
Matthews, J. M. & Sunde, M. Zinc fingers — folds for many occasions. IUBMB Life54, 351–355 (2002). ArticleCASPubMed Google Scholar
Gruss, H. J. & Dower, S. K. The TNF ligand superfamily and its relevance for human diseases. Cytokines Mol. Ther.1, 75–105 (1995). CASPubMed Google Scholar
Mallya, M., Campbell, R. D. & Aguado, B. Transcriptional analysis of a novel cluster of LY-6 family members in the human and mouse major histocompatibility complex: five genes with many splice forms. Genomics80, 113–123 (2002). ArticleCASPubMed Google Scholar
Milner, C. M. & Campbell, R. D. Structure and expression of the three MHC-linked HSP70 genes. Immunogenetics32, 242–251 (1990). ArticleCASPubMed Google Scholar
Gleimer, M. & Parham, P. Stress management: MHC class I and class I-like molecules as reporters of cellular stress. Immunity19, 469–477 (2003). ArticleCASPubMed Google Scholar
Alfonso, C. & Karlsson, L. Nonclassical MHC class II molecules. Annu. Rev. Immunol.18, 113–142 (2000). ArticleCASPubMed Google Scholar
Ohno, S. Evolution by Gene Duplication (Springer, New York, 1970). Book Google Scholar
Mazet, F. & Shimeld, S. M. Gene duplication and divergence in the early evolution of vertebrates. Curr. Opin. Genet. Dev.12, 393–396 (2002). ArticleCASPubMed Google Scholar
Flajnik, M. F. & Kasahara, M. Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity15, 351–362 (2001). ArticleCASPubMed Google Scholar
Sidow, A. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev.6, 715–722 (1996). ArticleCASPubMed Google Scholar
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001).
Hughes, A. L. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol. Biol. Evol.15, 854–870 (1998). ArticleCASPubMed Google Scholar
Abi-Rached, L., Gilles, A., Shiina, T., Pontarotti, P. & Inoko, H. Evidence of en bloc duplication in vertebrate genomes. Nature Genet.31, 100–105 (2002). The latest hypothesis to explain the MHC paralogy. ArticleCASPubMed Google Scholar
Rand, V. Genome evolution: a study of MHC paralogous genes in the human genome. Ph.D. Thesis, University of Cambridge, UK (2003). Access through http://www.sanger.ac.uk/Info/theses/
Kaufman, J. et al. The chicken B locus is a minimal essential major histocompatibility complex. Nature401, 923–925 (1999). ArticleCASPubMed Google Scholar
Rogers, S. & Kaufman, J. (personal communication).
Teng, M. S. et al. A human TAPBP (TAPASIN)-related gene, TAPBP-R. Eur. J. Immunol.32, 1059–1068 (2002). ArticleCASPubMed Google Scholar
Wagner, A. Selection and gene duplication: a view from the genome. Genome Biol.3, R1012 (2002). Article Google Scholar
Marsh, S. G. E., Parham, P. & Barber, L. D.The HLA Factsbook(Academic Press, San Diego, California, 2000). Google Scholar
Ahmad, T. et al. Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. Hum. Mol. Genet.12, 647–656 (2003). ArticleCASPubMed Google Scholar
Stenzel, A. et al. Patterns of linkage disequilibrium in the MHC region on human chromosome 6p.Hum. Genet.114, 377–385 (2004). ArticleCASPubMed Google Scholar
Trowsdale, J. & Parham, P. Mini-review: defense strategies and immunity-related genes. Eur. J. Immunol.34, 7–17 (2004). ArticleCASPubMed Google Scholar
Zdobnov, E. M. et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science298, 149–159 (2002). ArticleCASPubMed Google Scholar
Christophides, G. K. et al. Immunity-related genes and gene families in Anopheles gambiae. Science298, 159–165 (2002). ArticleCASPubMed Google Scholar
Lazarus, R. et al. Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease. Immunol. Rev.190, 9–25 (2002). ArticleCASPubMed Google Scholar
Vivier, E., Tomasello, E. & Paul, P. Lymphocyte activation via NKG2D: towards a new paradigm in immune recognition? Curr. Opin. Immunol.14, 306–311 (2002). ArticleCASPubMed Google Scholar
Lechler, R. & Warrens, A. HLA in Health and Disease (Academic Press, London, 2000). Google Scholar
Feder, J. N. et al. A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis.Nature Genet.13, 399–408 (1996). The authors describe a novel role for an MHC class I molecule. This is a landmark paper that illustrates the problems posed by linkage disequilibrium in disease mapping in the MHC. ArticleCASPubMed Google Scholar
von Kempis, J. Arthropathy in hereditary hemochromatosis. Curr. Opin. Rheumatol.13, 80–83 (2001). ArticleCASPubMed Google Scholar
Rubio, J. P. et al. Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis. Hum. Genet.114, 573–580 (2004). ArticleCASPubMed Google Scholar
Hellerbrand, C., Poppl, A., Hartmann, A., Scholmerich, J. & Lock, G. HFE C282Y heterozygosity in hepatocellular carcinoma: evidence for an increased prevalence.Clin. Gastroenterol. Hepatol.1, 279–284 (2003). ArticleCASPubMed Google Scholar
Pal, D. K. et al. BRD2 (RING3) is a probable major susceptibility gene for common juvenile myoclonic epilepsy. Am. J. Hum. Genet.73, 261–270 (2003). Identification of a promoter mutation within the MHC that is strongly linked to a common form of epilepsy. ArticleCASPubMedPubMed Central Google Scholar
Okamoto, K. et al. Identification of IκBL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am. J. Hum. Genet.72, 303–312 (2003). ArticleCASPubMed Google Scholar
Schmidt, A. M., Yan, S. D., Yan, S. F. & Stern, D. M. The biology of the receptor for advanced glycation end products and its ligands. Biochim. Biophys. Acta1498, 99–111 (2000). ArticleCASPubMed Google Scholar
Hofmann, M. A. et al. RAGE and arthritis: the G82S polymorphism amplifies the inflammatory response. Genes Immun.3, 123–135 (2002). ArticleCASPubMed Google Scholar
Bjorkman, P. J. et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature329, 506–512 (1987). ArticleCASPubMed Google Scholar
Brown, J. H. et al. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature364, 33–39 (1993). ArticleCASPubMed Google Scholar
Siebold, C. et al. Crystal structure of HLA-DQ0602 that protects against type 1 diabetes and confers strong susceptibility to narcolepsy.Proc. Natl Acad. Sci. USA101, 1999–2004 (2004). ArticleCASPubMedPubMed Central Google Scholar
Gao, X. et al. Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS.N. Engl. J. Med.344, 1668–1675 (2001).Along with reference 83, this paper shows how a single amino-acid change can influence structural and functional properties ofHLA-B27antigens, and inHLA-B35molecules is associated with rate of progression from HIV infection to AIDS. ArticleCASPubMed Google Scholar
Ferrara, G. B. et al. Bone marrow transplantation from unrelated donors: the impact of mismatches with substitutions at position 116 of the human leukocyte antigen class I heavy chain. Blood98, 3150–3155 (2001). ArticleCASPubMed Google Scholar
Doxiadis, I. I. et al. Association between specific HLA combinations and probability of kidney allograft loss: the taboo concept. Lancet348, 850–853 (1996). ArticleCASPubMed Google Scholar
Chen, T. C., Waldmann, H. & Fairchild, P. J. Induction of dominant transplantation tolerance by an altered peptide ligand of the male antigen Dby. J. Clin. Invest.113, 1754–1762 (2004).This paper shows that the balance of destructive and protective T cells in a transplant setting can be changed by using altered peptides for presentation by MHC molecules ArticleCASPubMedPubMed Central Google Scholar
Hansen, J. A. & Dupont, B. in Proceedings of the 13thInternational Histocompatibility Workshop and Congress (IHWG Press, Seattle, in the press).
Novik, K. L. et al. Epigenomics: genome-wide study of methylation phenomena. Curr. Issues Mol. Biol.4, 111–128 (2002). CASPubMed Google Scholar
Teitell, M. & Richardson, B. DNA methylation in the immune system. Clin. Immunol.109, 2–5 (2003). ArticleCASPubMed Google Scholar
Soen, Y., Chen, D. S., Kraft, D. L., Davis, M. M. & Brown, P. O. Detection and characterizationof cellular immune responses using peptide-MHC microarrays. PLoS Biol.1, E65 (2003). ArticlePubMedPubMed Central Google Scholar
Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCASPubMed Google Scholar
Vance, V. & Vaucheret, H. RNA silencing in plants — defense and counterdefense. Science292, 2277–2280 (2001). ArticleCASPubMed Google Scholar
Lecellier, C. H. & Voinnet, O. RNA silencing: no mercy for viruses? Immunol. Rev.198, 285–303 (2004). ArticleCASPubMed Google Scholar
Bock, G. & Goode, J. Immunoinformatics — Strategies for Better Understanding of Immune Function (Novartis Foundation, Chichester, UK, 2003). Book Google Scholar
Chabas, D., Taheri, S., Renier, C. & Mignot, E. The genetics of narcolepsy. Annu. Rev. Genomics Hum. Genet.4, 459–483 (2003). ArticleCASPubMed Google Scholar
Sollid, L. M. Coeliac disease: dissecting a complex inflammatory disorder. Nature Rev. Immunol.2, 647–655 (2002). ArticleCAS Google Scholar
Brown, N. P., Whittaker, A. J., Newell, W. R., Rawlings, C. J. & Beck, S. Identification and analysis of multigene families by comparison of exon fingerprints. J. Mol. Biol.249, 342–359 (1995). ArticleCASPubMed Google Scholar