Partial nucleotide sequence of a bovine major histocompatibility class II DR beta-like gene

A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA

The major histocompatibility complex (MHC) in mammals codes for antigen-presenting proteins. For this reason, the MHC is of great importance for immune function and animal health. Previous studies revealed this gene-dense and polymorphic region in river buffalo to be on the short arm of chromosome 2, which is homologous to cattle chromosome 23. Using cattle-derived STS markers and a river buffalo radiation hybrid (RH) panel (BBURH5000 ), we generated a high-resolution RH map of the river buffalo MHC region. The buffalo MHC RH map (cR5000 ) was aligned with the cattle MHC RH map (cR12000 ) to compare gene order. The buffalo MHC had similar organization to the cattle MHC, with class II genes distributed in two segments, class IIa and class IIb. Class IIa was closely associated with the class I and class III regions, and class IIb was a separate cluster. A total of 53 markers were distributed into two linkage groups based on a two-point LOD score threshold of ≥8. The first linkage group included 32 markers from class IIa, class I and class III. The second linkage group included 21 markers from class IIb. Bacterial artificial chromosome clones for seven loci were mapped by fluorescence in situ hybridization on metaphase chromosomes using single- and double-color hybridizations. The order of cytogenetically mapped markers in the region corroborated the physical order of markers obtained from the RH map and served as anchor points to align and orient the linkage groups.

Sequencing and genetic analysis of a bovine DQB cDNA clone

A BoLA-DQB cDNA clone (BoLA-DQ beta-1) was isolated by screening a bovine lymphoblastoid cDNA library with a HLA-DQB genomic clone. The DNA and predicted protein sequences were compared to class II sequences from cattle and other species. BoLA-DQ beta-1 has 92.0% similarity to the coding regions of two previously sequenced BoLA-DQB genomic clones and 69.6% similarity to a BoLA-DR beta pseudogene. However, the first domain encoded by BoLA-DQ beta-1 has 94 amino acids; one more than the predicted size of the products encoded by two previously sequenced bovine DQB genes (BoDQ beta-Q1 and BoDQ beta-Y1). Comparing all coding regions, BoLA-DQ beta-1 has greater nucleotide similarity to HLA-DQB sequences than to I-A beta, HLA-DRB and I-E beta sequences. Like the HLA-DQB gene product, the cytoplasmic domain of the predicted protein encoded by BoLA-DQ beta-1 is eight amino acids shorter than that of I-A beta, HLA-DRB and I-E beta molecules. Six clone-specific amino acid substitutions were identified in the beta 1 domain of BoLA-DQ beta-1, including an unusual cysteine residue at position 13 which is believed to be positioned on a beta-strand and face into the antigen recognition site. Southern blot analysis of PvuII-digested genomic DNA from a paternal half-sibling family (sire, and six dam-offspring pairs) using BoLA-DQ beta-1 as a probe, revealed five allelic PvuII RFLP patterns, including two patterns not previously described, that cosegregated with serologically-defined BoLA-A (class I) alleles. The evolution, polymorphism and function of a transcriptionally active BoLA-DQB gene can now be readily studied using this DQB cDNA clone as a source of allele and locus-specific oligonucleotide primers.

Nucleotide sequence and northern analysis of a bovine major histocompatibility class II DR beta-like cDNA

A 1.2-kb bovine DR beta-like cDNA clone (BoLA-DRB3) was isolated from a peripheral blood lymphocyte cDNA library utilizing a human DR beta cDNA as a probe. BoLA-DRB3 was found to have a high degree of nucleotide sequence similarity (96.8%) with a previously sequenced bovine DR beta-like gene (A1). It is believed that BoLA-DRB3 and A1 represent distinct alleles of one of the three bovine DR beta-like loci. Sequence comparison of BoLA-DRB3 with genes representing the other two bovine DR beta-like loci resulted in moderate degrees of sequence similarities (83.1% and 86.3%, respectively). Comparison of the relative abundance of RNA transcripts of the three bovine DR beta-like loci by Northern analysis of lymphocyte RNA indicated that BoLA-DRB3 is the most actively transcribed of the three bovine DR beta-like genes. Based on these results we suggest that of the three DR beta-like loci thus far identified in the bovine, only one is actively transcribed.

Restriction fragment length polymorphisms in bovine major histocompatibility complex class II beta-chain genes using bovine exon-containing hybridization probes

Restriction fragment length polymorphisms (RFLPs) have been identified in the bovine MHC class II region using five hybridization probes constructed from two bovine genomic clones. Four probes were constructed from a bovine DR beta-like gene, BoLA-DRB2. These included a probe containing the complete beta 1 exon (R2-beta 1), a probe containing the last 129 base pairs of the beta 2 exon (R2-beta 2), a probe containing intron immediately 5' of the beta 2 exon (R2-5' beta 2), and a probe containing the complete transmembrane exon (R2-TM). A fifth probe was constructed from a novel bovine beta-chain gene, BoLA-DIB, and contained the entire TM exon (I1-TM). R2-beta 1 defined very little polymorphism. R2-beta 2 hybridized to several fragments but one or two fragments hybridized much stronger on all Southern blots and it was presumed these corresponded to BoLA-DRB2 fragments. By using R2-5' beta 2 as a probe, these BoLA-DRB2 fragments were confirmed: 6.4 and 2.7-kb Eco RI alleles, 1.7- and 1.5-kb Pvu II alleles, 5.9-, 5.4-, 3.7- and 1.9-kb TaqI alleles, and a non-polymorphic 22.5-kb BamHI fragment. I1-TM identified three alleles with TaqI. To investigate the linkage between the RFLP alleles, 166 offspring of five sires were tested. Complete linkage was found for all RFLPs identified with the BoLA-DRB2 probes. However, the RFLP patterns of 13 calves out of 58 indicated recombination between BoLA-DRB2 and BoLA-DIB.

Organization and polymorphism of bovine major histocompatibility complex class II genes as revealed by genomic hybridizations with bovine probes

Previous studies on restriction fragment length polymorphism of bovine major histocompatibility complex class II genes have primarily been based on the use of human probes. In the present study bovine probes for DQA, DQB, DRB and DYA were used for RFLP analysis of cattle genomic DNA digested with PvuII and TaqI. There was an excellent agreement between the RFLP results obtained with homologous and heterologous probes. Although a few 'new' restriction fragments were revealed with the bovine probes there was no discrepancy with regard to the classification of allelic types with the two types of probes. The major advantages of using bovine probes were a better hybridization signal and reduced cross-hybridization between loci. Hybridization experiments with DQA probes for the first domain exon from two different genomic clones revealed the presence of two distinct types of bovine DQA genes. Surprisingly, these probes did not cross-hybridize at high stringency, indicating that the two genes are quite divergent. Hybridization with a recently described genomic clone for a novel bovine alpha-chain gene confirmed that it corresponds to the DYA gene which had previously been identified by cross-hybridization to a human DQA probe.

Cloning and sequence analysis of 14 DRB alleles of the bovine major histocompatibility complex by using the polymerase chain reaction

The genetic diversity in the first domain exon of a bovine class II DRB gene was investigated by PCR amplification and DNA sequencing. Genomic DNA samples representing 14 different class II haplotypes, defined by RFLP analysis, were used. The analysis revealed an extensive polymorphism and 14 alleles at a single locus, designated DRB3, were identified. Multiple amino acid substitutions were found in all pairwise comparisons of alleles; 5 to 21 substitutions in the 83 positions compared. The genetic diversity at the amino acid level found in cattle matches the one previously found in the DRB1 locus in man. The significantly higher frequency of replacement substitutions compared with the frequency of silent substitutions provides strong evidence that there is selection for genetic diversity in the bovine DRB3 first domain exon. A comparison of the DRB polymorphism in man and cattle reveals a striking similarity as regards the location of polymorphic positions in the DRB molecule and the degree of polymorphism at polymorphic positions. The majority of polymorphic positions in both species are found in the proposed antigen recognition site of the class II molecule. In addition, there are eight positions which are polymorphic in both species but have not been assigned to the antigen recognition site. The possible functional significance of the polymorphism of these latter positions is discussed.

Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti)

The molecular diversity and phylogenetic relationships of two class II genes of the baleen whale major histocompatibility complex were investigated and compared to toothed whales and out-groups. Amplification of the DQB exon 2 provided sequences showing high within-species and between-species nucleotide diversity and uninterrupted reading frames consistent with functional class II loci found in related mammals (e.g., ruminants). Cloning of amplified products indicated gene duplication in the humpback whale and triplication in the southern right whale, with average nucleotide diversity of 5.9 and 6.3%, respectively, for alleles of each species. Significantly higher nonsynonymous divergence at sites coding for peptide binding (32% for humpback and 40% for southern right) suggested that these loci were subject to positive (overdominant) selection. A population survey of humpback whales detected 23 alleles, differing by up to 21% of their inferred amino acid sequences. Amplification of the DRB exon 2 resulted in two groups of sequences. One was most similar to the DRB3 of the cow and present in all whales screened to date, including toothed whales. The second was most similar to the DRB2 of the cow and was found only in the bowhead and right whales. Both loci showed low diversity among species and apparent loss of function or altered function including interruption of reading frames. Finally, comparison of inferred protein sequence of the DRB3-like locus suggested convergence with the DQB, perhaps resulting from intergenic conversion or recombination.

Cattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb region

In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and -DOB genes enable these loci to be used as markers in genetic trait analyses.

Characterization of 18 new BoLA-DRB3 alleles

The second exon of the bovine MHC class II DRB3 gene was amplified by polymerase chain reaction (PCR) from DNA samples of 568 zebu Brahman cattle (Bos indicus) from Martinique (French West Indies). Cloning of these PCR products allowed the isolation of both alleles from each animal, which were characterized by the PCR-restriction fragment length polymorphism (RFLP) technique using the restriction enzymes RsaI, BstYI and HaeIII. Four new PCR-RFLP patterns were obtained by digestion with RsaI. These patterns were named 'v', 'w', 'x' and 'y' continuing the accepted nomenclature. Sequencing of each allele allowed the identification of 18 new BoLA-DRB3 exon 2 nucleotide sequences and their deduced amino acid sequences.

Sequence and PCR-RFLP analysis of 14 novel BoLA-DRB3 alleles

The genetic diversity of the bovine class II DRB3 locus was investigated by polymerase chain reaction (PCR) amplification and DNA sequencing of the first domain exon. Studying 34 animals of various cattle breeds, 14 previously unrecognized DRB3 alleles were identified. In three alleles, amino acid substitutions were observed that had not been previously found in bovine DRB3, but occurred at the same position in bovine DQB and in the DRB alleles of other mammals. For all newly identified alleles, the restriction fragment length polymorphism (RFLP) patterns of PCR products obtained with the enzymes RsaI, BstYI, and HaeIII were compared with patterns of 38 previously described alleles. Altogether, eleven novel PCR-RFLP types were defined. Twelve out of the 42 PCR-RFLP types identified so far were not found to be fully informative because they corresponded to more than one allelic sequence. PCR-RFLP may therefore be a rapid and useful method for DRB3 typing in cattle families, but for studies on outbred populations, sequencing and hybridization techniques are required.

Polymorphism of bovine MHC class II genes. Joint report of the Fifth International Bovine Lymphocyte Antigen (BoLA) Workshop, Interlaken, Switzerland, 1 August 1992

Polymorphism of the bovine DRB, DQA, DQB, DYA, DOB and DIB genes was investigated using restriction fragment length polymorphism (RFLP) analysis, isoelectric focusing (IEF), class II serology and polymerase chain reaction (PCR) based typing techniques. The simultaneous application of multiple typing techniques and the characterization of multiple genes resulted in a greatly enhanced picture of the bovine class II regions. Thirty-eight class IIa (DR-DQ) and 5 class IIb (DYA-DOB-DIB) haplotypes were defined. It was found that IEF types were associated with DRB3 polymorphism defined by DRB3 PCR-RFLP and DRB3 microsatellite PCR. Serologically defined polymorphism was associated with distinct molecular/IEF motifs and, therefore, DR and DQ specificities could be tentatively distinguished. Although the DR and DQ genes are tightly linked, neither DR nor DQ typing defined all of the class IIa region polymorphism. Furthermore, even the most powerful DRB3 typing technique, DRB3 PCR-RFLP, failed to detect all expressed DRB3 polymorphism. All detected DRB3 polymorphism could, however, be distinguished with a combination of two molecular techniques: DRB3 PCR-RFLP and DRB3 microsatellite PCR. RFLP typing with transmembrane probes detected significantly less polymorphism than typing with cDNA or exon probes. However, the transmembrane probes were useful because they were locus specific. The presence of only 5 of 12 possible class IIb haplotypes was unexpected and indicates that the DYA, DOB and DIB genes are tightly linked.

Strong association between polymorphisms in an intronic microsatellite and in the coding sequence of the BoLA-DRB3 gene: implications for microsatellite stability and PCR-based DRB3 typing

A highly polymorphic microsatellite in the bovine DRB3 gene was characterized by polymerase chain reaction (PCR) analysis and DNA sequencing. A very strong association between expressed DRB3 polymorphism and microsatellite alleles was revealed by PCR analysis of genomic DNA from 116 animals representing three breeds of cattle. The results indicated a low frequency of microsatellite length mutations as the association was consistent over breeds. The DRB3 microsatellite may be utilized in a PCR-based typing method of bovine class II alleles. The microsatellite polymorphism did not distinguish all known DRB3 alleles, but it was shown that this method may be complemented by the use of allele-specific PCR based on the extensive polymorphism in the DRB3 exon 2. The DNA sequences of seven microsatellite alleles, associated with different class II haplotypes, were determined. The DRB3 microsatellite is composed of three repeat motifs, a stretch of at least 10 uninterrupted (TG)n dinucleotides, a long but interrupted stretch of (GA)n dinucleotides, and a few (CAGA)n tetranucleotides. There were pronounced sequence differences between alleles and the results indicated that the evolution of this microsatellite has involved length mutations of the dinucleotide repeats as well as point mutations causing interruptions in the dinucleotide repeats.

Extensive polymorphism of the BoLA-DRB3 gene distinguished by PCR-RFLP

A polymerase chain reaction (PCR)-based method is described for typing of alleles of the bovine lymphocyte antigen (BoLA)-DRB3 gene. A total of 30 DRB3 alleles were distinguished by digestion of PCR amplification products of BoLA-DRB3 exon 2 with RsaI, BstYI and HaeIII (PCR-RFLP). All restriction fragment patterns, with the exception of one HaeIII pattern, were consistent with restriction sites that were found among 14 previously sequenced DRB3 alleles. The PCR-RFLP typing method was evaluated on 168 genomic DNA samples collected from animals of 10 cattle breeds, 48 of which were typed in the Fourth International BoLA Workshop for BoLA-DRB and -DQ by conventional restriction fragment length polymorphism (RFLP) analysis using heterologous and homologous DNA probes. Thirty-one DRB/DQ haplotypes containing 23 DRB3 alleles were identified among the 48 workshop animals analysed. Using PCR-RFLP, 11 DRB3 alleles were identified in 18 workshop animals for which DRB RFLPs were not informative. PCR-RFLP typing of additional animals revealed five new DRB3 alleles, of which three contained a putatively located three basepair deletion in the identical position as found for the sequenced allele DRB*2A. PCR-RFLP was shown to be a rapid and sensitive method for the detection of polymorphism in a functionally relevant domain of the BoLA-DRB3 gene and should be useful for studying the evolution of DRB polymorphism in cattle and other Bovidae.

BoLA-DIB: species distribution, linkage with DOB, and northern analysis

The bovine major histocompatibility complex differs from that of other species in that it has a second group of class II genes that are separated from the classical class I/class II complex by 15 to 20 centimorgans. Two class II bovine genes, BoLA-DYA and BoLA-DIB, seem to be unique based on sequence analysis. To investigate the occurrence of one of these genes, BoLA-DIB, in other species, a DIB 2nd domain exon probe was hybridized to Southern genomic blots containing DNA from representatives from a variety of mammalian families. The probe hybridized only with DNA from representatives of the Cervidae, Giraffidae and Bovidae families, indicating that significant sequence similarity to DIB may be confined to these families. Analysis of the linkage relationship between DIB and DOB in cattle half-sib families did not yield any recombinants among 39 informative offspring, indicating that DIB maps within the second group of class II bovine genes; DOB has previously been mapped to the second group of class II genes. A 1st domain exon probe from BoLA-DQB hybridized to RNA from either stimulated or unstimulated peripheral bovine lymphocytes, while 1st domain exon probes from BoLA-DIB and HLA-DOB gave no hybridization signals, indicating that transcription in peripheral lymphocytes of these genes is at least very minor compared to BoLA-DQB.

The nucleotide sequence and evolution of ovine MHC class II B genes: DQB and DRB

The nucleotide sequences of one Ovar-DQB gene, excluding exon 1 and parts of the introns, and one Ovar-DRB pseudogene are presented. The structure of the Ovar-DQB gene is typical of a major histocompatibility complex (MHC) class II B gene and demonstrates considerable sequence similarity with that of humans including such characteristics as the less common polyadenylation signal, ATTAAA. The ovine sequence has a typical 5' acceptor splice signal for exon 5, thus potentially encoding a full length cytoplasmic tail. The Ovar-DRB gene identified in this study was found to be a pseudogene, lacking a defined exon 2 and containing premature termination codons in both exons 3 and 4. The 3' donor splice site of exon 3 is also atypical. A purine-pyrimidine microsatellite repeat, (dC.dA)15, in the 3' region of the pseudogene may be a hotspot for recombination within the ovine DR subregion.

Partial nucleotide sequence of a novel bovine major histocompatibility complex class II beta-chain gene, BoLA-DIB

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.