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Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing. Immunogenetics 2016; 68:765-781. [PMID: 27516207 PMCID: PMC5056950 DOI: 10.1007/s00251-016-0945-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/19/2016] [Indexed: 12/12/2022]
Abstract
The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
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Oliver RA, Brown P, Spooner RL, Joosten I, Williams JL. The analyses of antigen and DNA polymorphism within the bovine major histocompatibility complex: 1. The class I antigens. Anim Genet 2009; 20:31-41. [PMID: 2567136 DOI: 10.1111/j.1365-2052.1989.tb00839.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Serology, isoelectric focusing (IEF) of expressed antigens, and restriction fragment length polymorphisms (RFLP) were compared for the identification of BoLA class I haplotypes. Expressed antigens identified as bands by IEF correlated well with serological definition confirming and extending our earlier findings (Joosten et al. 1988). Comparison of serology and isoelectric focusing bands with restriction fragments was more complicated; fragments were found which correlated both with broadly reacting and antigen specific sera. We also found correlation of fragments with two or more sera which showed no cross-reactivity. Fragments unique to particular haplotypes were also observed. Serology remains the simplest method of typing BoLA class I antigens. Isoelectric focusing generally agrees with serological definition of antigens and detects antigens not yet defined by serology. It may also be useful in defining the products of other expressed BoLA class I loci. In order to identify RFLPs which could be used for typing, comparison with serology or IEF is essential. Haplotype specific RFLPs could be useful in identifying genes linked to the MHC.
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Affiliation(s)
- R A Oliver
- AFRC Institute of Animal Physiology and Genetics Research, Edinburgh Research Station, UK
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Babiuk S, Horseman B, Zhang C, Bickis M, Kusalik A, Schook LB, Abrahamsen MS, Pontarollo R. BoLA class I allele diversity and polymorphism in a herd of cattle. Immunogenetics 2007; 59:167-76. [PMID: 17206412 DOI: 10.1007/s00251-006-0173-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Accepted: 10/24/2006] [Indexed: 10/23/2022]
Abstract
Major histocompatibility complex class I genes are among the most polymorphic genes characterized. The high level of polymorphism is essential for generating host immune responses. In humans, three distinct genomic loci encode human leukocyte antigen (HLA) class I genes, allowing individuals to express up to six different HLA class I molecules. In cattle, the number of distinct genomic loci are currently at least six, and the number of different bovine leukocyte antigens (BoLA) class I molecules that are expressed in individual animals are variable. The extent of allele variation within the cattle population is unknown. In this study, the number and variety of BoLA class I sequences expressed by 36 individuals were determined from full-length BoLA class I cDNA clones. Twenty distinct BoLA class I alleles were identified, with only four being previously reported. The number of expressed BoLA class I alleles in individual animals ranged between one and four, with none of the animals having an identical complement of BoLA class I molecules. Variation existed in the number of BoLA class I alleles expressed as well as the composition of expressed alleles, however, several BoLA class I alleles were found in multiple individual animals. Polymorphic amino acid sites were analyzed for positive and negative selection using the ADAPTSITE program. In the antigen recognition sites (ARS), there were eight positions that were predicted to be under positive selection and three positions that were predicted to be under negative selection from 62 positions. In contrast, for non-antigen recognition sites (non-ARS), there were three positions that were predicted to be under positive selection and 20 that were predicted to be under negative selection from 278, indicating that positive selection of amino acids occurs at a greater frequency within the antigen recognition sites.
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Affiliation(s)
- Shawn Babiuk
- Pyxis Genomics Canada, Saskatoon, Saskatchewan, Canada.
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4
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Ellis SA, Staines KA, Stear MJ, Hensen EJ, Morrison WI. DNA typing for BoLA class I using sequence-specific primers (PCR-SSP). Int J Immunogenet 1998. [DOI: 10.1111/j.1744-313x.1998.tb01154.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Russell GC, Oliver RA, Sawhney SM. Cloning, transfection, and DNA sequence of a second gene from the BoLA-A11 haplotype. Immunogenetics 1996; 44:315-8. [PMID: 8753865 DOI: 10.1007/bf02602564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- G C Russell
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
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Sawhney SM, Hopkins J, Spooner RL, Russell GC. A novel expression vector for transfection of bovine MHC class I genes. Gene 1996; 171:281-4. [PMID: 8666287 DOI: 10.1016/0378-1119(96)00096-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A vector is described for the expression of genomic or cDNA copies of bovine major histocompatibility complex (MHC) class I genes in transfected mouse Ltk- cells. Class I gene fragments are amplified by the polymerase chain reaction, using primers in conserved parts of exon 2 and the 3'-untranslated region of the gene. Amplified class I gene fragments can then be subcloned into the expression vector, pBoLA-21, which contains the necessary 5'- and 3'-sequences for correct expression. The vector was tested by subcloning and expressing genomic and cDNA clones.
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Affiliation(s)
- S M Sawhney
- Division of Molecular Biology, Roslin Institute, Midlothian, UK
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Bamford AI, Douglas A, Friede T, Stevanovic S, Rammensee HG, Adair BM. Peptide motif of a cattle MHC class I molecule. Immunol Lett 1995; 45:129-36. [PMID: 7622180 DOI: 10.1016/0165-2478(94)00244-l] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A consensus motif for a bovine major histocompatibility complex (MHC) class I molecule, A20, was derived from parainfluenza type-3 (PI-3) virus-infected muscle-derived fibroblast cells and peripheral blood leukocytes by extraction of the naturally processed peptides from MHC class I molecules by treatment with TFA and peptide sequencing of the complex mixture. The results showed that the majority of peptides were 9 amino acids long with position 2 occupied by lysine and position 9 occupied by arginine. The arginine at position 9 suggests that cattle, like humans, but unlike the mouse have permissive TAP transporter molecules accepting peptides with positively charged amino acids at their C-terminus. This is the first report of a MHC ligand motif in cattle.
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Affiliation(s)
- A I Bamford
- DKFZ, Department of Tumour Virus Immunology, Heidelberg I, Germany
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Becker Y. Need for cellular and humoral immune responses in bovines to ensure protection from foot-and-mouth disease virus (FMDV)--a point of view. Virus Genes 1994; 8:199-214. [PMID: 7975267 DOI: 10.1007/bf01703078] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The published studies on immunization of experimental animals, cattle, and sheep with synthetic peptides containing the antigenic domains in FMDV structural protein VP1 were analyzed. The results obtained with various FMDV synthetic peptides designed to stimulate the humoral immune response in bovines were compared to the current knowledge on MHC class I and class II, and the properties of the peptide binding grooves in each of them. X-ray crystallography of MHC class I proteins provided the three-dimensional structure of the peptide binding groove and led to the isolation and identification of "self" and viral peptides that naturally associate with the peptide binding grooves of both types of MHC and HLA molecules. The available knowledge of the amino acid motifs in MHC and HLA class I-bound viral peptides priming the CD8+ cytotoxic T cell responses must be coupled with the understanding of the three-dimensional structure of BoLA class I. This would aid in the development of an experimental approach to induce bovine anti-FMDV CD8+ cytotoxic cells to complement the humoral immune response to FMDV, which is currently achieved by a killed virus vaccine and, at the experimental level, by a peptide vaccine. Stimulation of both cellular and humoral immune responses against FMDV in cattle may reduce the risk of disease and virus shedding.
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Affiliation(s)
- Y Becker
- Department of Molecular Virology, Faculty of Medicine, Hebrew University of Jerusalem, Israel
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Ellis SA. MHC studies in domestic animals. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 1994; 21:209-15. [PMID: 9098434 DOI: 10.1111/j.1744-313x.1994.tb00194.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- S A Ellis
- Agricultural and Food Research Council, Institute for Animal Health, Compton, UK
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al-Murrani SW, Glass EJ, Hopkins J. BoLA class I charge heterogeneity reflects the expression of more than two loci. Anim Genet 1994; 25:165-72. [PMID: 7943950 DOI: 10.1111/j.1365-2052.1994.tb00105.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Internationally recognized allo-antisera in lymphocyte microcytotoxicity assays are thought to detect allelic products of a single highly polymorphic class I locus. A recent report suggested that two bovine lymphocyte antigen (BoLA) class I loci are expressed at the protein level. However, 1D-IEF analysis of BoLA class I molecules reveals multi-band patterns which cannot be reconciled with the reported number of loci. The aim of this study was to investigate the origins of the charge diversity of BoLA class I molecules observed using 1D-IEF. BoLA class I molecules appear to be glycosylated at a single N-linked position with a complex type carbohydrate moiety which has up to three terminal sialic acid residues. Class I molecules immunoprecipitated from resting bovine PBL are not phosphorylated. Neither modification is responsible for the observed charge heterogeneity. Peptide mapping reveals that different BoLA charge variants have distinct digestion patterns. Furthermore, a number of different polypeptides are associated with each serological specificity. These polypeptides appear to be encoded by different loci which exist in linkage disequilibrium. The number of charge variants with different peptide maps indicates that the BoLA system has a minimum of three class I loci expressed at the protein level.
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Affiliation(s)
- S W al-Murrani
- Division of Molecular Biology, Roslin Institute, Midlothian, UK
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Garber TL, Hughes AL, Letvin NL, Templeton JW, Watkins DI. Sequence and evolution of cattle MHC class I cDNAs: concerted evolution has not taken place in cattle. Immunogenetics 1993; 38:11-20. [PMID: 8462989 DOI: 10.1007/bf00216385] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To explore genetic mechanisms responsible for major histocompatibility complex (MHC) class I evolution in the artiodactyls, we cloned and sequenced MHC class I cDNAs from a Bos taurus bull heterozygous for cattle MHC (BoLA) class I serological specificities w2 and w30. Four unique cDNAs were found, indicating the presence of at least two MHC class I loci. Analysis of these four cDNAs and all previously published BoLA cDNA sequences suggested that there may be three cattle MHC class I loci. Additionally, comparison of all of the BoLA class I cDNAs to MHC class I cDNAs of other artiodactyls showed that some of the BoLA class I cDNAs were more similar to certain sheep cDNAs than they were to other cattle cDNAs. These data indicate that each BoLA class I locus has evolved independently after an ancestral gene duplication event and that inter-locus segmental exchange or concerted evolution has not occurred rapidly enough to cause extensive divergence between the orthologous MHC class I loci of sheep and cattle.
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Affiliation(s)
- T L Garber
- Texas A & M University, Department of Veterinary Pathobiology, College Station 77843
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Affiliation(s)
- R Fries
- Department of Animal Science, Swiss Federal Institute of Technology, Zurich
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Ellis SA, Braem KA, Morrison WI. Transmembrane and cytoplasmic domain sequences demonstrate at least two expressed bovine MHC class I loci. Immunogenetics 1992; 37:49-56. [PMID: 1428011 DOI: 10.1007/bf00223544] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have used the polymerase chain reaction to amplify cDNA from expressed bovine major histocompatibility complex class I genes. Sequences obtained from transmembrane and cytoplasmic domains were used to identify the number of expressed alleles. Data from three animals suggest that there are four major expressed alleles, representing the products of two (or more) loci. We have also demonstrated the presence of an alternatively spliced mRNA, which has been observed in five animals. The alternative splicing removes exon 7 (the major site of class I phosphorylation), which predicts a truncated molecule with a cytoplasmic portion 16 amino acids shorter than usual. This phenomenon was detected for only a single class I allele within each individual.
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Affiliation(s)
- S A Ellis
- Institute for Animal Health, Compton, Nr Newbury, Berks, UK
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Stone RT, Muggli-Cockett NE. Partial nucleotide sequence of a novel bovine major histocompatibility complex class II beta-chain gene, BoLA-DIB. Anim Genet 1990; 21:353-60. [PMID: 2128591 DOI: 10.1111/j.1365-2052.1990.tb01980.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A bovine genomic clone that hybridized to HLA-DQ beta cDNA was isolated and fragments containing the beta 1, beta 2 and transmembrane (TM) exons subcloned. The nucleotide sequences of the exons and flanking intron regions were determined. Comparisons of these exon nucleotide sequences and derived amino acid sequences to human class II beta-chain sequences showed that this gene is only 77% identical to HLA-DQ beta and about 75% identical to bovine DQ beta-like genes. The exon sequences were more divergent from other class II beta-chain genes. However, structural features such as conserved cysteines and regions of amino acids strongly suggest this to be a class II beta-chain gene. When exon-containing fragments were used as hybridization probes on Southern blots of bovine genomic DNA digested with Eco RI or Pvu II, each exon hybridized to a single band. Based on these results we have referred to this gene as a novel bovine class II beta-chain gene, BoLA-DIB.
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Affiliation(s)
- R T Stone
- USDA-ARS, US Meat Animal Research Center, Clay Center, Nebraska 68933
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Grossberger D, Hein W, Marcuz A. Class I major histocompatibility complex cDNA clones from sheep thymus: alternative splicing could make a long cytoplasmic tail. Immunogenetics 1990; 32:77-87. [PMID: 2397935 DOI: 10.1007/bf00210444] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To investigate the class I major histocompatibility complex (MHC) genes expressed in the young sheep thymus, a cDNA library was screened with a human HLA-B7 cDNA probe under conditions of relaxed stringency. Thirteen clones were isolated and found by partial sequences to fall into five classes, requiring the expression of at least three loci. One sequence was found six times, almost half of the total, and may thus represent the major message expressed in the young sheep thymus. One of the clones was found to have failed to excise the intron between cytoplasmic exons 7 and 8, leading to the predicted synthesis of a cytoplasmic domain 23 amino acids longer than the other sheep sequences, and 15 amino acids longer than any cytoplasmic domain previously described. The sequences of all the clones were found to be most similar to bovine, and least similar to mouse class I MHC sequences.
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