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Shiina T, Blancher A, Inoko H, Kulski JK. Comparative genomics of the human, macaque and mouse major histocompatibility complex. Immunology 2016; 150:127-138. [PMID: 27395034 DOI: 10.1111/imm.12624] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 12/20/2022] Open
Abstract
The MHC is a highly polymorphic genomic region that encodes the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. The MHC locus was first discovered in the mouse and for the past 50 years it has been studied most intensively in both mice and humans. However, in recent years the macaque species have emerged as some of the more important and advanced experimental animal models for biomedical research into MHC with important human immunodeficiency virus/simian immunodeficiency virus and transplantation studies undertaken in association with precise MHC genotyping and haplotyping methods using Sanger sequencing and next-generation sequencing. Here, in this special issue on 'Macaque Immunology' we provide a short review of the genomic similarities and differences among the human, macaque and mouse MHC class I and class II regions, with an emphasis on the association of the macaque class I region with MHC polymorphism, haplotype structure and function.
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Affiliation(s)
- Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Antoine Blancher
- Laboratoire d'Immunogénétique moléculaire (LIMT, EA 3034), Laboratoire d'immunologie, Faculté de Médecine Purpan, Université Toulouse 3, CHU de Toulouse, Toulouse, France
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, WA, Australia
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Guidry PA, Stroynowski I. The murine family of gut-restricted class Ib MHC includes alternatively spliced isoforms of the proposed HLA-G homolog, "blastocyst MHC". THE JOURNAL OF IMMUNOLOGY 2005; 175:5248-59. [PMID: 16210630 DOI: 10.4049/jimmunol.175.8.5248] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The gastrointestinal tract is populated by a multitude of specialized immune cells endowed with receptors for classical (class Ia) and nonclassical (class Ib) MHC proteins. To identify class I products that engage these receptors and impact immunity/tolerance, we studied gut-transcribed class Ib loci and their polymorphism in inbred, outbred, and wild-derived mice. Intestinal tissues enriched in epithelial cells contained abundant transcripts of ubiquitously expressed and preferentially gut-restricted Q and T class I loci. The latter category included the "blastocyst Mhc" gene, H2-Bl, and its putative paralog, Tw5. Expression of H2-Bl was previously detected only at the maternal/fetal interface, where it was proposed to induce immune tolerance via interactions with CD94/NKG2A receptors. Analysis of coding region polymorphism performed here revealed two major alleles of H2-Bl with conserved residues at positions critical for class I protein folding and peptide binding. Both divergent alleles are maintained in outbred and wild mice under selection for fecundity and pathogen resistance. Surprisingly, we found that alternative splicing of H2-Bl mRNA in gut tissues is prevalent and allele-specific. It leads to strain-dependent expression of diverse repertoires of canonical and noncanonical transcripts that may give rise to distinct ligands for intestinal NK cell, T cell, and/or intraepithelial lymphocyte receptors.
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Affiliation(s)
- Paula A Guidry
- Center for Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9093, USA
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Howcroft TK, Singer DS. Expression of nonclassical MHC class Ib genes: comparison of regulatory elements. Immunol Res 2003; 27:1-30. [PMID: 12637766 DOI: 10.1385/ir:27:1:1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Peptide binding proteins of the major histocompatibility complex consist of the "classical" class Ia and "nonclassical" class Ib genes. The gene organization and structure/function relationship of the various exons comprising class I proteins are very similar among the class Ia and class Ib genes. Although the tissue-specific patterns of expression of these two gene families are overlapping, many class Ib genes are distinguished by relative low abundance and/or limited tissue distribution. Further, many of the class Ib genes serve specialized roles in immune responses. Given that the coding sequences of the class Ia and class Ib genes are highly homologous we sought to examine the promoter regions of the various class Ib genes by comparison to the well characterized promoter elements regulating expression of the class Ia genes. This analysis revealed a surprising complexity of promoter structures among all class I genes and few instances of conservation of class Ia promoter regulatory elements among the class Ib genes.
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Affiliation(s)
- T Kevin Howcroft
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA.
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Crew MD, Bates LM. Sequence, expression, and polymorphism of the Peromyscus leucopus Mhc class Ib gene, M4. Immunogenetics 2003; 55:95-9. [PMID: 12700875 DOI: 10.1007/s00251-003-0569-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Revised: 03/18/2003] [Indexed: 10/25/2022]
Abstract
The H2 M region harbors about 20 class I genes or gene fragments the function of which are largely obscure. The rat Mhc ( RT1) appears to contain several orthologs of H2 M region genes although orthologs in more distantly related species have yet to be clearly identified. In this report, the sequence of a genomic clone containing a Peromyscus leucopus Mhc ( Pele) class I gene is presented and based on sequence similarity was found to be the Pele ortholog of H2-M4. Unlike H2-M4, which is a pseudogene, PeleM4 appeared to be an intact Mhc class Ib gene. Appropriately splice PeleM4 mRNA transcripts were detected in the liver, lung, and thymus. Polymorphism of PeleM4 was examined by sequencing exon 2 and 3 of the PeleM4 gene from seven different Pele haplotypes and six PeleM4 alleles were identified. These results suggest that the existence of some H2 M region class Ib genes predates the divergence of Peromyscus and Mus genera which occurred 40-60 million years ago and provide an example of unique pathways in the evolution of Mhc class Ib genes.
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Affiliation(s)
- Mark D Crew
- Central Arkansas Veterans Healthcare System and Departments of Microbiology and Immunology and Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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Takada T, Kumánovics A, Amadou C, Yoshino M, Jones EP, Athanasiou M, Evans GA, Fischer Lindahl K. Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex. Genome Res 2003; 13:589-600. [PMID: 12671000 PMCID: PMC430170 DOI: 10.1101/gr.975303] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have determined the complete sequence of 951,695 bp from the class I region of H2, the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotype bc). The sequence contains 26 genes. The sequence spans from the last 50 kb of the H2-T region, including 2 class I genes and 3 class I pseudogenes, and includes the H2-M region up to Gabbr1. A 500-kb stretch of the H2-M region contains 9 class I genes and 4 pseudogenes, which fall into two subfamilies, M1 and M10, distinct from other mouse class I genes. This M1/M10 class I gene-cluster is separated from the centromeric H2-T and the telomeric H2-M4, -5 and -6 class I genes by "nonclass I genes". Comparison with the corresponding 853-kb region of the human Mhc, which includes the HLA-A region, shows a mosaic of conserved regions of orthologous nonclass I genes separated by regions of species-specific expansion of paralogous Mhc class I genes. The analysis of this mosaic structure illuminates the dynamic evolution of the Mhc class I region among mammals and provides evidence for the framework hypothesis.
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Affiliation(s)
- Toyoyuki Takada
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Loconto J, Papes F, Chang E, Stowers L, Jones EP, Takada T, Kumánovics A, Fischer Lindahl K, Dulac C. Functional expression of murine V2R pheromone receptors involves selective association with the M10 and M1 families of MHC class Ib molecules. Cell 2003; 112:607-18. [PMID: 12628182 DOI: 10.1016/s0092-8674(03)00153-3] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vomeronasal organ (VNO) of the mouse has two neuronal compartments expressing distinct families of pheromone receptors, the V1Rs and the V2Rs. We report here that two families of major histocompatibility complex (MHC) class Ib molecules, the M10 and the M1 families, show restricted expression in V2R-expressing neurons. Our data suggest that neurons expressing a given V2R specifically co-express one or a few members of the M10 family. Biochemical and immunocytochemical analysis demonstrates that in VNO sensory dendrites M10s belong to large multi-molecular complexes that include pheromone receptors and beta2-microglobulin (beta2m). In cultured cells, M10s appear to function as escort molecules in transport of V2Rs to the cell surface. Accordingly, beta2m-deficient mice exhibit mislocalization of V2Rs in the VNO and a specific defect in male-male aggressive behavior. The functional characterization of M10 highlights an unexpected role for MHC molecules in pheromone detection by mammalian VNO neurons.
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Affiliation(s)
- Jennifer Loconto
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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Ishii T, Hirota J, Mombaerts P. Combinatorial coexpression of neural and immune multigene families in mouse vomeronasal sensory neurons. Curr Biol 2003; 13:394-400. [PMID: 12620187 DOI: 10.1016/s0960-9822(03)00092-7] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones in higher vertebrates. In mouse and rat, two gene superfamilies, V1r and V2r vomeronasal receptor genes, are expressed in sensory neurons whose cell bodies are located in, respectively, the apical and basal layers of the VNO epithelium. Here, we report that neurons of the basal layer express another multigene family, termed H2-Mv, representing nonclassical class I genes of the major histocompatibility complex. The nine H2-Mv genes are expressed differentially in subsets of neurons. More than one H2-Mv gene can be expressed in an individual neuron. In situ hybridization with probes for H2-Mv and V2r genes reveals complex and nonrandom combinations of coexpression. While neural expression of Mhc class I molecules is increasingly being appreciated, the H2-Mv family is distinguished by variegated expression across seemingly similar neurons and coexpression with a distinct multigene family encoding neural receptors. Our findings suggest that basal vomeronasal sensory neurons may consist of multiple lineages or compartments, defined by particular combinations of V2r and H2-Mv gene expression.
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Affiliation(s)
- Tomohiro Ishii
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Abstract
Major histocompatibility complex class Ib molecules may play a surprising role in pheromone detection in mammals.
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Affiliation(s)
- Kristin Scott
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Forman J, Lindahl KF. Listing, location, binding motifs, and expression of nonclassical class I and related genes and molecules. CURRENT PROTOCOLS IN IMMUNOLOGY 2002; Appendix 1:Appendix 1M. [PMID: 18432863 DOI: 10.1002/0471142735.ima01ms49] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The tables presented in this appendix list nonclassical class I or related genes/molecules arranged by the chromosomal region where they are encoded. This includes genes that fall into the Ib region of the murine major histocompatibility complex (MHC) which includes H2-Q, -T, and -M, as well as CD1, which lies outside the MHC region. A final table includes genes/molecules that are encoded in diverse regions. They are included in this section because they are either class I related in that their heavy chain is related to classical class I and/or they are associated with ion given is for the C57BL/6 (B6) strain unless otherwise noted.
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Affiliation(s)
- James Forman
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Lambracht-Washington D, Wonigeit K, Lindahl KF. Gene order of the RT1.M region of the rat MHC exemplifies interspecies conservation with the mouse. Transplant Proc 1999; 31:1515-6. [PMID: 10330986 DOI: 10.1016/s0041-1345(99)00022-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- D Lambracht-Washington
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA
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