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Garcia AA, Plain KM, Thomson PC, Thomas AJ, Davies CJ, Toribio JALML, Whittington RJ. Association between major histocompatibility complex haplotypes and susceptibility of unvaccinated and vaccinated cattle to paratuberculosis. Vet Immunol Immunopathol 2023; 265:110677. [PMID: 37952345 DOI: 10.1016/j.vetimm.2023.110677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Bovine Johne's disease (BJD) or paratuberculosis is caused by Mycobacterium avium spp. paratuberculosis (MAP) and is a worldwide problem among domestic and wild ruminants. While vaccines are available, natural differences in background immunity between breeds within species and between individuals within herds suggest that genetic differences may be able to be exploited in marker-assisted selection as an aid to disease control. The major histocompatibility complex (MHC) is an important component in immune recognition with considerable genetic variability. In this study, associations between the MHC and resistance to BJD were explored in dairy cattle across two herds in which some of the cattle had been vaccinated with Silirum® (n = 540 cows). A BJD susceptible animal was exposed to MAP and became infected, while a resistant animal was exposed but did not become infected. There are different ways to define both exposure and infection, with different levels of stringency, therefore many classifications of the same set of animals are possible and were included in the analysis. The polymorphic regions of major histocompatibility complex class I (MHC I) and class II (MHC II) genes were amplified from the genomic DNA by PCR and sequenced, targeting exons 2 and 3 of the classical and non-classical MHC I genes and exon 2 from the DRB3, DQA1, DQA2 + 3 and DQB MHC II genes. The frequencies of MHC I and MHC II haplotypes and alleles were determined in susceptible and resistant populations. In unvaccinated animals, seven MHC I haplotypes and seven MHC II haplotypes were associated with susceptibility while two MHC I and six MHC II haplotypes were associated with resistance (P < 0.05). In vaccinated animals, two MHC I and three MHC II haplotypes were associated with susceptibility, while one MHC I and two MHC II haplotypes were associated with resistance (P < 0.05). The alleles in significant haplotypes were also identified. Case definitions with higher stringency resulted in fewer animals being included in the analyses, but the power to detect an association was not reduced and there was an increase in strength and consistency of associations. Consistent use of stringent case definitions is likely to improve agreement in future association studies.
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Affiliation(s)
- Anabel A Garcia
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Karren M Plain
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Peter C Thomson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Jenny-Ann L M L Toribio
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Richard J Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia.
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Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
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Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
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Schwartz JC, Maccari G, Heimeier D, Hammond JA. Highly-contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I. HLA 2021; 99:167-182. [PMID: 34802191 DOI: 10.1111/tan.14494] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3' end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3' coding sequence, we identified distinct subgroups of BoLA-3 and BoLA-6 that represent distinct genetic loci. We further examined allele-specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, UK.,Anthony Nolan Research Institute, London, UK
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Rapacz-Leonard A, Leonard M, Chmielewska-Krzesińska M, Paździor-Czapula K, Janowski T. Major histocompatibility complex class I in the horse (Equus caballus) placenta during pregnancy and parturition. Placenta 2018; 74:36-46. [PMID: 30638631 DOI: 10.1016/j.placenta.2018.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/07/2018] [Accepted: 12/15/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Major histocompatibility protein class I (MHC-I) is believed to be expressed in the horse allantochorion only in limited areas at limited times. However, its expression has only been investigated in early pregnancy with non-quantitative techniques that cannot reliably detect small amounts of protein. OBJECTIVE To quantify the relative expression of MHC-I in the allantochorion and endometrium during days 90-240 of pregnancy (PREG), parturition with physiological delivery of fetal membranes (PHYS), and parturition with retention of these membranes (FMR). Also, to visualize protein expression and determine whether classical or non-classical MHC-I mRNA is expressed. ANIMALS Heavy draft horses. SETTING PREG horses (n = 12) were sampled postmortem at a slaughterhouse. PHYS (n = 6) and FMR (n = 5) horses were sampled at farms in the vicinity of Olsztyn, Poland. METHODS For relative quantification of MHC-I, western blotting with densitometry was used. To visualize MHC-I, immunohistochemistry was used. For mRNA identification, RT-PCR was performed. RESULTS Although the quantity of MHC-I was lower during PREG than parturition, it was present in the allantochorion and endometrium during PREG. During parturition, MHC-I expression was upregulated in the allantochorion (PHYS vs. PREG: 2.7-times higher, 95% confidence interval, 1.3- to 5.7-times higher; FMR vs. PREG: 3.2-times higher, 95% confidence interval, 1.5- to 6.7-times higher). At parturition, staining for MHC-I was detected in the microcotyledons. Classical and non-classical MHC-I were expressed in both tissues during PREG, PHYS, and FMR. CONCLUSION MHC-I protein is present in the horse allantochorion and endometrium for at least the first two-thirds of pregnancy and at parturition.
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Affiliation(s)
- A Rapacz-Leonard
- Department of Animal Reproduction with Clinic, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Poland.
| | - M Leonard
- University of Warmia and Mazury, Olsztyn, Poland
| | - M Chmielewska-Krzesińska
- Department of Pathophysiology, Forensic Veterinary and Administration, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Poland
| | - K Paździor-Czapula
- Department of Pathological Anatomy, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Poland
| | - T Janowski
- Department of Animal Reproduction with Clinic, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Poland
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Kasonta R, Mauritz J, Spohr C, Sauter-Louis C, Duchow K, Cussler K, Holsteg M, Bastian M. Bovine Neonatal Pancytopenia-Associated Alloantibodies Recognize Individual Bovine Leukocyte Antigen 1 Alleles. Front Immunol 2018; 9:1902. [PMID: 30154800 PMCID: PMC6102493 DOI: 10.3389/fimmu.2018.01902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/01/2018] [Indexed: 11/13/2022] Open
Abstract
Bovine neonatal pancytopenia (BNP) was a vaccine-induced alloimmune disease observed in young calves and characterized by hemorrhages, pancytopenia, and severe destruction of the hematopoietic tissues. BNP was induced by alloreactive maternal antibodies present in the colostrum of certain cows vaccinated with a highly adjuvanted vaccine against bovine viral diarrhea. Bioprocess impurities, originating from the production cell line of the vaccine, are likely to have induced these alloreactive antibodies. One prominent alloantigen recognized by vaccine-induced alloantibodies is highly polymorphic bovine major histocompatibility complex class I antigen (bovine leukocyte antigen 1-BoLA I). Aim of this study was to define the fine specificity of BNP-associated anti-BoLA I alloantibodies. In total, eight different BoLA I alleles from the production cell line were identified. All genes were cloned and recombinantly expressed in murine cell lines. Using these cells in a flow cytometric assay, the presence of BoLA I specific alloantibodies in BNP dam sera was proven. Three BoLA I variants were identified that accounted for the majority of vaccine-induced BoLA I reactivity. By comparing the sequence of immunogenic to non-immunogenic BoLA I variants probable minimal epitopes on BoLA I were identified. In general, dams of BNP calves displayed high levels of BoLA I reactive alloantibodies, while vaccinated cows delivering healthy calves had significantly lower alloantibody titers. We identified a subgroup of vaccinated cows with healthy calves displaying very high alloantibody titers. Between these cows and BNP dams no principle difference in the BoLA I reactivity pattern was observed. However, with a limited set of dam-calf pairs it could be demonstrated that serum from these cows did not bind to BoLA I expressing leukocytes of their offspring. By contrast, when testing cells from surviving BNP calves with the corresponding dam's serum there was significant binding. We therefore conclude that predominantly highly alloreactive cows are at risk to induce BNP and it depends on the paternally inherited BoLA I whether or not the calf develops BNP.
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Affiliation(s)
| | | | | | | | | | | | - Mark Holsteg
- Landwirtschaftskammer Nordrhein-Westfalen, Bonn, Germany
| | - Max Bastian
- Paul-Ehrlich-Institut, Langen, Germany.,Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Shi B, Thomas AJ, Benninghoff AD, Sessions BR, Meng Q, Parasar P, Rutigliano HM, White KL, Davies CJ. Genetic and epigenetic regulation of major histocompatibility complex class I gene expression in bovine trophoblast cells. Am J Reprod Immunol 2017; 79. [PMID: 29131441 PMCID: PMC5728445 DOI: 10.1111/aji.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022] Open
Abstract
Problem The regulatory mechanisms governing differential expression of classical major histocompatibility complex (MHC) class I (MHC‐Ia) and non‐classical MHC class I (MHC‐Ib) genes are poorly understood. Method of study Quantitative reverse transcription‐ polymerase chain reaction (PCR) was used to compare the abundance of MHC‐I transcripts and related transcription factors in peripheral blood mononuclear cells (PBMC) and placental trophoblast cells (PTC). Methylation of MHC‐I CpG islands was detected by bisulfite treatment and next‐generation sequencing. Demethylation of PBMC and PTC with 5′‐aza‐deoxycytidine was used to assess the role of methylation in gene regulation. Results MHC‐I expression was higher in PBMC than PTC and was correlated with expression of IRF1, class II MHC transactivator (CIITA), and STAT1. The MHC‐Ia genes and BoLA‐NC1 were devoid of CpG methylation in PBMC and PTC. In contrast, CpG sites in the gene body of BoLA‐NC2, ‐NC3, and ‐NC4 were highly methylated in PBMC but largely unmethylated in normal PTC and moderately methylated in somatic cell nuclear transfer PTC. In PBMC, demethylation resulted in upregulation of MHC‐Ib by 2.8‐ to 6‐fold, whereas MHC‐Ia transcripts were elevated less than 2‐fold. Conclusion DNA methylation regulates bovine MHC‐Ib expression and is likely responsible for the different relative levels of MHC‐Ib to MHC‐Ia transcripts in PBMC and PTC.
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Affiliation(s)
- Bi Shi
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Benjamin R Sessions
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Parveen Parasar
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
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Parasar P, Wilhelm A, Rutigliano HM, Thomas AJ, Teng L, Shi B, Davis WC, Suarez CE, New DD, White KL, Davies CJ. Expression of bovine non-classical major histocompatibility complex class I proteins in mouse P815 and human K562 cells. Res Vet Sci 2016; 107:161-170. [PMID: 27473990 DOI: 10.1016/j.rvsc.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/20/2016] [Accepted: 06/06/2016] [Indexed: 11/16/2022]
Abstract
Major histocompatibility complex class I (MHC-I) proteins can be expressed as cell surface or secreted proteins. To investigate whether bovine non-classical MHC-I proteins are expressed as cell surface or secreted proteins, and to assess the reactivity pattern of monoclonal antibodies with non-classical MHC-I isoforms, we expressed the MHC proteins in murine P815 and human K562 (MHC-I deficient) cells. Following antibiotic selection, stably transfected cell lines were stained with H1A or W6/32 antibodies to detect expression of the MHC-I proteins by flow cytometry. Two non-classical proteins (BoLA-NC1*00501 and BoLA-NC3*00101) were expressed on the cell surface in both cell lines. Surprisingly, the BoLA-NC4*00201 protein was expressed on the cell membrane of human K562 but not mouse P815 cells. Two non-classical proteins (BoLA-NC1*00401, which lacks a transmembrane domain, and BoLA-NC2*00102) did not exhibit cell surface expression. Nevertheless, Western blot analyses demonstrated expression of the MHC-I heavy chain in all transfected cell lines. Ammonium-sulfate precipitation of proteins from culture supernatants showed that BoLA-NC1*00401 was secreted and that all surface expressed proteins where shed from the cell membrane by the transfected cells. Interestingly, the surface expressed MHC-I proteins were present in culture supernatants at a much higher concentration than BoLA-NC1*00401. This comprehensive study shows that bovine non-classical MHC-I proteins BoLA-NC1*00501, BoLA-NC3*00101, and BoLA-NC4*00201 are expressed as surface isoforms with the latter reaching the cell membrane only in K562 cells. Furthermore, it demonstrated that BoLA-NC1*00401 is a secreted isoform and that significant quantities of membrane associated MHC-I proteins can be shed from the cell membrane.
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Affiliation(s)
- Parveen Parasar
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Amanda Wilhelm
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Lihong Teng
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Bi Shi
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - William C Davis
- Department of Veterinary Microbiology and Pathology, P.O. Box 647040, Washington State University, Pullman, WA, USA
| | - Carlos E Suarez
- USDA-ARS Animal Disease Research Unit, P.O. Box 646630, Washington State University, Pullman, WA, USA
| | - Daniel D New
- Department of Veterinary Microbiology and Pathology, P.O. Box 647040, Washington State University, Pullman, WA, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA.
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8
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Demasius W, Weikard R, Hadlich F, Buitkamp J, Kühn C. A novel RNAseq-assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease. BMC Genomics 2016; 17:365. [PMID: 27188848 PMCID: PMC4869273 DOI: 10.1186/s12864-016-2688-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/30/2016] [Indexed: 12/02/2022] Open
Abstract
Background MHC class I genotyping is essential for a wide range of biomedical, immunological and biodiversity applications. Whereas in human a comprehensive MHC class I allele catalogue is available, respective data in non-model species is scarce in spite of decades of research. Results Taking advantage of the new high-throughput RNA sequencing technology (RNAseq), we developed a novel RNAseq-assisted method (RAMHCIT) for MHC class I typing at nucleotide level. RAMHCIT is performed on white blood cells, which highly express MHC class I molecules enabling reliable discovery of new alleles and discrimination of closely related alleles due to the high coverage of alleles with reads. RAMHCIT is more comprehensive than previous methods, because no targeted PCR pre-amplification of MHC loci is necessary, which avoids preselection of alleles as usually encountered, when amplification with MHC class I primers is performed prior to sequencing. In addition to allele identification, RAMHCIT also enables quantification of MHC class I expression at allele level, which was remarkably consistent across individuals. Conclusions Successful application of RAMHCIT is demonstrated on a data set from cattle with different phenotype regarding a lethal, vaccination-induced alloimmune disease (bovine neonatal pancytopenia), for which MHC class I alleles had been postulated as causal agents. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2688-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wiebke Demasius
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Johannes Buitkamp
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586, Grub, Germany
| | - Christa Kühn
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
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Siva Subramaniam N, Morgan EF, Wetherall JD, Stear MJ, Groth DM. A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region. BMC Genomics 2015; 16:810. [PMID: 26480943 PMCID: PMC4613773 DOI: 10.1186/s12864-015-1992-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms. The revised map is more similar to Bovidae maps than the previous sheep maps and also includes several genes previously not annotated in the Chinese Merino BAC assembly and others not currently annotated in the sheep reference chromosome 20. In particular, the organisation of nonclassical MHC class I genes is similar to that present in the cattle MHC. Sequence analysis and prediction of amino acid sequences of MHC class I classical and nonclassical genes was performed and it was observed that the map contained one classical and eight nonclassical genes together with three possible pseudogenes. Conclusions The comprehensive physical map of the sheep MHC class I region enhances our understanding of the genetic architecture of the class I MHC region in sheep and will facilitate future studies of MHC function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1992-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N Siva Subramaniam
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - E F Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - J D Wetherall
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - M J Stear
- Department of Animal Production and Public Health, Faculty of Veterinary Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,Institute of Biodiversity, Animal Health and Comparative Medicine, Garscube Estate, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - D M Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
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Schwartz JC, Hammond JA. The assembly and characterisation of two structurally distinct cattle MHC class I haplotypes point to the mechanisms driving diversity. Immunogenetics 2015; 67:539-44. [PMID: 26227296 PMCID: PMC4539362 DOI: 10.1007/s00251-015-0859-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022]
Abstract
In cattle, there are six classical MHC class I genes that are variably present between different haplotypes. Almost all known haplotypes contain between one and three genes, with an allele of Gene 2 present on the vast majority. However, very little is known about the sequence and therefore structure and evolutionary history of this genomic region. To address this, we have refined the MHC class I region in the Hereford cattle genome assembly and sequenced a complete A14 haplotype from a homozygous Holstein. Comparison of the two haplotypes revealed extensive variation within the MHC class Ia region, but not within the flanking regions, with each gene contained within a conserved 63- to 68-kb sequence block. This variable region appears to have undergone block gene duplication and likely deletion at regular breakpoints, suggestive of a site-specific mechanism. Phylogenetic analysis using complete gene sequences provided evidence of allelic diversification via gene conversion, with breakpoints between each of the extracellular domains that were associated with high guanine-cytosine (GC) content. Advancing our knowledge of cattle MHC class I evolution will help inform investigations of cattle genetic diversity and disease resistance.
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Affiliation(s)
- John C Schwartz
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
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11
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Dos Santos LS, da Silva Mol JP, de Macedo AA, Silva APC, Dos Santos Ribeiro DL, Santos RL, da Paixão TA, de Carvalho Neta AV. Transcription of non-classic major histocompatibility complex (MHC) class I in the bovine placenta throughout gestation and after Brucella abortus infection. Vet Immunol Immunopathol 2015; 167:166-70. [PMID: 26188737 DOI: 10.1016/j.vetimm.2015.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 06/19/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Transcription of non-classical major histocompatibility complex class I (MHC-I) was assessed in the bovine placenta throughout gestation. Additionally, the effect of Brucella abortus infection on expression of non-classical MHC-I was also evaluated using a chorioallantoic membrane explant model of infection. The non-classical MHC-I genes MICB and NC3 had higher levels of transcription in the intercotyledonary region when compared to the placentome, which had higher levels of transcription at the second trimester of gestation. NC1 and classical MHC-I had very low levels of transcription throughout gestation. Trophoblastic cells of B. abortus-infected chorioallantoic membrane explants had an increase in transcription of non-classical MHC-I at 4h post infection. Therefore, this study provides an analysis of non-classical MHC-I transcription at different stages of gestation and different placental tissues, and during B. abortus infection. These findings provide additional knowledge on immune regulation in placental tissues, a known immune-privileged site.
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Affiliation(s)
| | - Juliana Pinto da Silva Mol
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Auricélio Alves de Macedo
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Patrícia Carvalho Silva
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Renato Lima Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tatiane Alves da Paixão
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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12
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Svitek N, Nzau B, Steinaa L, Nene V. A method to discriminate between closely related bovine major histocompatibility complex class I alleles by combining established PCR-SSP assays with RFLPs. ACTA ACUST UNITED AC 2015; 85:278-82. [PMID: 25789713 DOI: 10.1111/tan.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 11/22/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022]
Abstract
We have developed a polymerase chain reaction-sequence-specific primers-restriction fragment length polymorphism (PCR-SSP-RFLP) method to rapidly differentiate between the A18 and A18 variant (v) BoLA haplotypes and between A14 and A15/A15v BoLA haplotypes in Holstein/Friesian cattle. We used published SSP to PCR amplify BoLA alleles expressed in animals of known haplotype and exposed the amplicons to the restriction enzyme PvuII that was predicted to cut at a unique site in the middle of BoLA-6*01302 (A18v) and BoLA-1*00901 (A15) but not in BoLA-6*01301 (A18) or BoLA-1*02301 (A14) alleles. Whereas the method does not discriminate between the A15 and A15v haplotypes, as the BoLA-1*00902 allele associated with A15v also contains a PvuII site, we are interested in cattle of A18 and A14 haplotype for vaccine related studies. Our results also indicated that the BoLA-6*01302 (A18v) allele is much more abundant than BoLA-6*01301 (A18) in the cattle that we sampled.
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Affiliation(s)
- N Svitek
- International Livestock Research Institute (ILRI), Vaccine Biosciences, Nairobi 00100, Kenya
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13
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Ellis SA, Hammond JA. The functional significance of cattle major histocompatibility complex class I genetic diversity. Annu Rev Anim Biosci 2013; 2:285-306. [PMID: 25384144 DOI: 10.1146/annurev-animal-022513-114234] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Current concerns about food security highlight the importance of maintaining productive and disease-resistant livestock populations. Major histocompatibility complex (MHC) class I genes have a central role in immunity. A high level of diversity in these genes allows populations to survive despite exposure to rapidly evolving pathogens. This review aims to describe the key features of MHC class I genetic diversity in cattle and to discuss their role in disease resistance. Discussion centers on data derived from the cattle genome sequence and studies addressing MHC class I gene expression and function. The impact of intensive selection on MHC diversity is also considered. A high level of complexity in MHC class I genes and functionally related gene families is revealed. This highlights the need for increased efforts to determine key genetic components that govern cattle immune responses to disease, which is increasingly important in the face of changing human and environmental demands.
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Affiliation(s)
- Shirley A Ellis
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom; ,
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14
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Isolation and characterization of class I MHC genes in the giant panda (Ailuropoda melanoleuca). CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-012-5582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Babik W, Kawałko A, Wójcik JM, Radwan J. Low Major Histocompatibility Complex Class I (MHC I) Variation in the European Bison (Bison bonasus). J Hered 2012; 103:349-59. [DOI: 10.1093/jhered/ess005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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16
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Codner GF, Birch J, Hammond JA, Ellis SA. Constraints on haplotype structure and variable gene frequencies suggest a functional hierarchy within cattle MHC class I. Immunogenetics 2012; 64:435-45. [DOI: 10.1007/s00251-012-0612-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/13/2012] [Indexed: 12/11/2022]
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17
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Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes? Immunogenetics 2012; 64:475-80. [PMID: 22419150 DOI: 10.1007/s00251-012-0611-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 12/12/2022]
Abstract
The cattle major histocompatibility complex (MHC) region contains a variable number of classical class I genes encoding polymorphic molecules involved in antigen presentation. Six classical class I genes have been described, but assigning sequences to these genes has proved problematic. We propose a refinement of the existing nomenclature, which currently names the 97 known classical class I sequences in a single series. Phylogenetic analysis of the 3' portion of the coding region allows segregation of these into six groups; thus, we have prefixed existing names with the appropriate number. Although it is clear that some of these groups correspond to discrete genes, it is currently not possible to state definitively that all do. However, the main groupings are consistent, and in conjunction with other evidence, we feel it is now appropriate to rename the sequences accordingly. Segregation of sequences into groups in this way will facilitate ongoing research and future use of the cattle MHC section of the Immuno Polymorphism Database.
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18
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Regulation of non-classical major histocompatability complex class I mRNA expression in bovine embryos. J Reprod Immunol 2011; 91:31-40. [DOI: 10.1016/j.jri.2011.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 05/10/2011] [Accepted: 05/17/2011] [Indexed: 01/28/2023]
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Deutskens F, Lamp B, Riedel CM, Wentz E, Lochnit G, Doll K, Thiel HJ, Rümenapf T. Vaccine-induced antibodies linked to bovine neonatal pancytopenia (BNP) recognize cattle major histocompatibility complex class I (MHC I). Vet Res 2011; 42:97. [PMID: 21878124 PMCID: PMC3180656 DOI: 10.1186/1297-9716-42-97] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 08/30/2011] [Indexed: 01/26/2023] Open
Abstract
A mysterious disease affecting calves, named bovine neonatal pancytopenia (BNP), emerged in 2007 in several European countries. Epidemiological studies revealed a connection between BNP and vaccination with an inactivated vaccine against bovine virus diarrhea (BVD). Alloantibodies reacting with blood leukocytes of calves were detected in serum and colostrum of dams, which have given birth to calves affected by BNP. To understand the linkage between vaccination and the development of alloantibodies, we determined the antigens reacting with these alloantibodies. Immunoprecipitation of surface proteins from bovine leukocytes and kidney cells using sera from dams with a confirmed case of BNP in their gestation history reacted with two dominant protein species of 44 and 12 kDa. These proteins were not detected by sera from dams, free of BVDV and not vaccinated against BVD, and from sera of animals vaccinated with a different inactivated BVD vaccine. The 44 kDa protein was identified by mass spectrometry analysis as MHC I, the other as β-2-microglobulin. The presence of major histocompatibility complex class I (MHC I) in the vaccine was confirmed by Western blot using a MHC I specific monoclonal antibody. A model of BNP pathogenesis is proposed.
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Affiliation(s)
- Fabian Deutskens
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Benjamin Lamp
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Christiane M Riedel
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Eveline Wentz
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Günter Lochnit
- Institute of Biochemistry, Justus-Liebig-University Giessen, Germany
| | - Klaus Doll
- Clinic for Ruminants, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Heinz-Jürgen Thiel
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
| | - Till Rümenapf
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Germany
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20
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21
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Hu R, Lemonnier G, Bourneuf E, Vincent-Naulleau S, Rogel-Gaillard C. Transcription variants of SLA-7, a swine non classical MHC class I gene. BMC Proc 2011; 5 Suppl 4:S10. [PMID: 21645289 PMCID: PMC3108204 DOI: 10.1186/1753-6561-5-s4-s10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In pig, very little information is available on the non classical class I (Ib) genes of the Major Histocompatibility Complex (MHC) i.e. SLA-6, -7 and -8. Our aim was to focus on the transcription pattern of the SLA-7 gene. RT-PCR experiments were carried out with SLA-7 specific primers targeting either the full coding sequence (CDS) from exon 1 to the 3 prime untranslated region (3UTR) or a partial CDS from exon 4 to the 3UTR. We show that the SLA-7 gene expresses a full length transcript not yet identified that refines annotation of the gene with eight exons instead of seven as initially described from the existing RefSeq RNA. These two RNAs encode molecules that differ in cytoplasmic tail length. In this study, another SLA-7 transcript variant was characterized, which encodes a protein with a shorter alpha 3 domain, as a consequence of a splicing site within exon 4. Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant. An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon. In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.
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Affiliation(s)
- Rui Hu
- INRA, UMR de Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
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22
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Kusza S, Flori L, Gao Y, Teillaud A, Hu R, Lemonnier G, Bosze Z, Bourneuf E, Vincent-Naulleau S, Rogel-Gaillard C. Transcription specificity of the class Ib genes SLA-6, SLA-7 and SLA-8 of the swine major histocompatibility complex and comparison with class Ia genes. Anim Genet 2011; 42:510-20. [PMID: 21906102 DOI: 10.1111/j.1365-2052.2010.02170.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Our aim was to analyse the transcription levels of the three non-classical class Ib genes SLA-6, SLA-7 and SLA-8 of the swine major histocompatibility complex in various tissues and conditions and to compare them to the transcription levels of classical class Ia genes. Twenty-five adult tissues from two pig breeds, pig renal PK15 cells infected with the Pseudorabies virus, and peripheral blood mononuclear cells (PBMCs) stimulated by lipopolysaccharide or a mixture of phorbol myristate acetate and ionomycin were included in our study. Relative transcription was quantified by quantitative real-time PCR. On average, in adult tissues and PBMCs and compared to SLA-6, the transcription level of SLA-Ia genes was 100-1000 times higher, the level of SLA-8 was 10-20 times higher, and that of SLA-7 was five times higher. Thus, SLA-8 is the most transcribed SLA-Ib gene, followed by the SLA-7 and SLA-6 genes. The highest transcription levels of SLA-Ib transcripts were found in the lymphoid organs, followed by the lung and the digestive tract. The tissue variability of expression levels was widest for the SLA-6 gene, with a 1:32 ratio between the lowest and highest levels in contrast to a 1:12 ratio for the SLA-7 and SLA-8 genes and a 1:16 ratio for the SLA-Ia genes. During PK-15 infection and PBMC stimulation, SLA-Ia and SLA-8 genes were downregulated, whereas SLA-6 and SLA-7 were upregulated, downregulated or not significantly modified. Our overall results confirm the tissue-wide transcription of the three SLA-Ib genes and suggest that they have complementary roles.
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Affiliation(s)
- S Kusza
- Institute of Animal Science, University Debrecen, Centre for Agricultural and Applied Economic Sciences, 4032 Debrecen, Böszörményi Str.138, Hungary
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23
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O'Gorman GM, Al Naib A, Naib AA, Ellis SA, Mamo S, O'Doherty AM, Lonergan P, Fair T. Regulation of a bovine nonclassical major histocompatibility complex class I gene promoter. Biol Reprod 2010; 83:296-306. [PMID: 20427761 DOI: 10.1095/biolreprod.109.082560] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Studies have shown in humans and other species that the major histocompatibility complex class I (MHC-I) region is involved at a number of levels in the establishment and maintenance of pregnancy. The aim of this study was to characterize how a bovine nonclassical MHC-I gene (NC1) is regulated. Initial serial deletion experiments of a 2-kb fragment of the NC1 promoter identified regions with positive regulatory elements in the proximal promoter and evidence for a silencer module(s) further upstream that cooperatively contributed to constitutive NC1 expression. The cytokines interferon tau (IFNT), interferon gamma (IFNG), and interleukin 4 (IL4) significantly increased luciferase expression in NC1 promoter reporter constructs and endogenous NC1 mRNA levels in a bovine endometrial cell line. In addition, IFNG, IL3, IL4, and progesterone significantly increased Day 7 bovine blastocyst NC1 mRNA expression when supplemented during in vitro embryo culture. Site-directed mutagenesis analysis identified a STAT6 binding site that conferred IL4 responsiveness in the NC1 proximal promoter. Furthermore, methylation treatment of the proximal promoter, which contains a CpG island, completely abrogated constitutive NC1 expression. Overall, the findings presented here suggest that constitutive NC1 expression is regulated positively by elements in the proximal promoter, which are further controlled by upstream silencer modules. The promoter is responsive to IFNT, IFNG, and IL4, suggesting possible roles for these cytokines in bovine preimplantation embryo survival and/or maternal-fetal tolerance. Our studies also suggest that methylation of the proximal promoter, in particular, could play a significant role in regulating NC1 expression.
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Affiliation(s)
- Grace M O'Gorman
- School of Agriculture, Food Science & Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
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24
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Tallmadge RL, Campbell JA, Miller DC, Antczak DF. Analysis of MHC class I genes across horse MHC haplotypes. Immunogenetics 2010; 62:159-72. [PMID: 20099063 DOI: 10.1007/s00251-009-0420-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Accepted: 12/12/2009] [Indexed: 11/28/2022]
Abstract
The genomic sequences of 15 horse major histocompatibility complex (MHC) class I genes and a collection of MHC class I homozygous horses of five different haplotypes were used to investigate the genomic structure and polymorphism of the equine MHC. A combination of conserved and locus-specific primers was used to amplify horse MHC class I genes with classical and nonclassical characteristics. Multiple clones from each haplotype identified three to five classical sequences per homozygous animal and two to three nonclassical sequences. Phylogenetic analysis was applied to these sequences, and groups were identified which appear to be allelic series, but some sequences were left ungrouped. Sequences determined from MHC class I heterozygous horses and previously described MHC class I sequences were then added, representing a total of ten horse MHC haplotypes. These results were consistent with those obtained from the MHC homozygous horses alone, and 30 classical sequences were assigned to four previously confirmed loci and three new provisional loci. The nonclassical genes had few alleles and the classical genes had higher levels of allelic polymorphism. Alleles for two classical loci with the expected pattern of polymorphism were found in the majority of haplotypes tested, but alleles at two other commonly detected loci had more variation outside of the hypervariable region than within. Our data indicate that the equine major histocompatibility complex is characterized by variation in the complement of class I genes expressed in different haplotypes in addition to the expected allelic polymorphism within loci.
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Affiliation(s)
- Rebecca L Tallmadge
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Doyle J, Ellis SA, O’Gorman GM, Aparicio Donoso IM, Lonergan P, Fair T. Classical and non-classical Major Histocompatibility Complex class I gene expression in in vitro derived bovine embryos. J Reprod Immunol 2009; 82:48-56. [DOI: 10.1016/j.jri.2009.06.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 06/12/2009] [Accepted: 06/17/2009] [Indexed: 10/20/2022]
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26
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Genomic location and characterisation of MIC genes in cattle. Immunogenetics 2008; 60:477-83. [PMID: 18548244 DOI: 10.1007/s00251-008-0306-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/16/2008] [Indexed: 01/02/2023]
Abstract
Major histocompatibility complex (MHC) class I chain-related (MIC) genes have been previously identified and characterised in human. They encode polymorphic class I-like molecules that are stress-inducible, and constitute one of the ligands of the activating natural killer cell receptor NKG2D. We have identified three MIC genes within the cattle genome, located close to three non-classical MHC class I genes. The genomic position relative to other genes is very similar to the arrangement reported in the pig MHC region. Analysis of MIC cDNA sequences derived from a range of cattle cell lines suggest there may be four MIC genes in total. We have investigated the presence of the genes in distinct and well-defined MHC haplotypes, and show that one gene is consistently present, while configuration of the other three genes appears variable.
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