Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes

Donald Miller, Rebecca L. Tallmadge, Matthew Binns, Baoli Zhu, Yasmin Ali Mohamoud, Ayeda Ahmed, Samantha A. Brooks, Douglas F. Antczak

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.

Original languageEnglish
Pages (from-to)145-156
Number of pages12
JournalImmunogenetics
Volume69
Issue number3
DOIs
Publication statusPublished - 1 Mar 2017

Fingerprint

Major Histocompatibility Complex
Haplotypes
Horses
HLA Antigens
MHC Class II Genes
Genes
Horse Diseases
CD45 Antigens
MHC Class I Genes
Bacterial Artificial Chromosomes
Genomic Library
Terminator Codon
DNA Sequence Analysis
varespladib methyl
Amino Acid Sequence

Keywords

  • Genetics
  • Horse
  • Immunity
  • Major histocompatibility complex
  • Polymorphism

ASJC Scopus subject areas

  • Immunology
  • Genetics

Cite this

Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes. / Miller, Donald; Tallmadge, Rebecca L.; Binns, Matthew; Zhu, Baoli; Ali Mohamoud, Yasmin; Ahmed, Ayeda; Brooks, Samantha A.; Antczak, Douglas F.

In: Immunogenetics, Vol. 69, No. 3, 01.03.2017, p. 145-156.

Research output: Contribution to journalArticle

Miller, D, Tallmadge, RL, Binns, M, Zhu, B, Ali Mohamoud, Y, Ahmed, A, Brooks, SA & Antczak, DF 2017, 'Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes', Immunogenetics, vol. 69, no. 3, pp. 145-156. https://doi.org/10.1007/s00251-016-0964-4
Miller, Donald ; Tallmadge, Rebecca L. ; Binns, Matthew ; Zhu, Baoli ; Ali Mohamoud, Yasmin ; Ahmed, Ayeda ; Brooks, Samantha A. ; Antczak, Douglas F. / Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes. In: Immunogenetics. 2017 ; Vol. 69, No. 3. pp. 145-156.
@article{10b53885024a46b4aebd1bb473cd5138,
title = "Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes",
abstract = "The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.",
keywords = "Genetics, Horse, Immunity, Major histocompatibility complex, Polymorphism",
author = "Donald Miller and Tallmadge, {Rebecca L.} and Matthew Binns and Baoli Zhu and {Ali Mohamoud}, Yasmin and Ayeda Ahmed and Brooks, {Samantha A.} and Antczak, {Douglas F.}",
year = "2017",
month = "3",
day = "1",
doi = "10.1007/s00251-016-0964-4",
language = "English",
volume = "69",
pages = "145--156",
journal = "Immunogenetics",
issn = "0093-7711",
publisher = "Springer Verlag",
number = "3",

}

TY - JOUR

T1 - Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes

AU - Miller, Donald

AU - Tallmadge, Rebecca L.

AU - Binns, Matthew

AU - Zhu, Baoli

AU - Ali Mohamoud, Yasmin

AU - Ahmed, Ayeda

AU - Brooks, Samantha A.

AU - Antczak, Douglas F.

PY - 2017/3/1

Y1 - 2017/3/1

N2 - The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.

AB - The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.

KW - Genetics

KW - Horse

KW - Immunity

KW - Major histocompatibility complex

KW - Polymorphism

UR - http://www.scopus.com/inward/record.url?scp=84997170532&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84997170532&partnerID=8YFLogxK

U2 - 10.1007/s00251-016-0964-4

DO - 10.1007/s00251-016-0964-4

M3 - Article

VL - 69

SP - 145

EP - 156

JO - Immunogenetics

JF - Immunogenetics

SN - 0093-7711

IS - 3

ER -