Felipe Figueroa

H-2 haplotypes, genes and antigens: Second listing - II. The H-2 complex

In this second part of the Second Listing, we describe genes that constitute the H-2 complex proper. Here, we define the complex functionally as consisting of class I and class II loci (see Klein et al. 1983a). The H-2-associated complement loci and the Neu-1 locus have been described in the first part of the Second Listing (Klein et al. 1982), but for completeness we list them here again in some of the tables. We include into the H-2 complex the cluster of Qa and Tla loci, which we consider as class I loci (Klein et al. 1983). The genetic map of the definitely established loci appears in Figure 1 and is based on the recent results of molecular genetics studies (Steinmetz et al. 1982 a, b). For historical reasons we also describe loci (regions, subregions) that were once thought to be part of the H-2 complex but either they have since been withdrawn, or their actual existence is at present uncertain. We first list loci (regions, subregions) that have been designated by capital letters (we call it Madmans Alphabet because of the frivolity with which symbols have been introduced and then withdrawn again), and then other loci believed to be associated with the H-2 complex. As in the First Listing (Klein et al. 1978), the core of the review in the Second Listing constitutes the tables of H-2 haplotypes, antigens, and determinants.

Mapping of Mhc class I and class II regions to different linkage groups in the zebrafish, Danio rerio

Abstract The mammalian major histocompatibility complex (Mhc) consists of three closely linked regions, I, II, and III, occupying a single chromosomal segment. The class I loci in region I and the class II loci in region II are related in their structure, function, and evolution. Region III, which is intercalated between regions I and II, contains loci unrelated to the class I and II loci, and to one another. There are indications that a similar Mhc organization exists in birds and amphibians. Here, we demonstrate that in the zebrafish (Danio rerio), a representative of the teleost fishes, the class II loci are divided between two linkage groups which are distinct from the linkage group containing the class I loci. The β2-microglobulin-encoding gene is loosely linked to one of the class II loci. The gene coding for complement factor B, which is one of the region III genes in mammals, is linked neither to the class I nor to the class II loci in the zebrafish. These results, combined with preliminary data suggesting that the class I and class II regions in another order of teleost fish are also in different linkage groups, indicate that close linkage of the two regions is not necessary either for regulation of expression or for co-evolution of the class I and class II loci. They also raise the question of whether linkage of the class I and class II loci in tetrapods is a primitive or derived character.

Nonlinkage of major histocompatibility complex class I and class II loci in bony fishes.

Abstract In tetrapods, the functional (classical) class I and class II B loci of the major histocompatibility complex (Mhc) are tightly linked in a single chromosomal region. In an earlier study, we demonstrated that in the zebrafish, Danio rerio, order Cypriniformes, the two classes are present on different chromosomes. Here, we show that the situation is similar in the stickleback, Gasterosteus aculeatus, order Gasterosteiformes, the common guppy, Poecilia reticulata, order Cyprinodontiformes, and the cichlid fish Oreochromis niloticus, order Perciformes. These data, together with unpublished results from other laboratories suggest that in all Euteleostei, the classical class I and class II B loci are in separate linkage groups, and that in at least some of these taxa, the class II loci are in two different groups. Since Euteleostei are at least as numerous as tetrapods, in approximately one-half of jawed vertebrates, the class I and class II regions are not linked.

H-2 haplotypes, genes and antigens: Second listing

In this second part of the Second Listing, we describe genes that constitute the H-2 complex proper. Here, we define the complex functionally as consisting of class I and class II loci (see Klein et al. 1983a). The H-2-associated complement loci and the Neu-1 locus have been described in the first part of the Second Listing (Klein et al. 1982), but for completeness we list them here again in some of the tables. We include into the H-2 complex the cluster of Qa and Tla loci, which we consider as class I loci (Klein et al. 1983). The genetic map of the definitely established loci appears in Figure 1 and is based on the recent results of molecular genetics studies (Steinmetz et al. 1982 a, b). For historical reasons we also describe loci (regions, subregions) that were once thought to be part of the H-2 complex but either they have since been withdrawn, or their actual existence is at present uncertain. We first list loci (regions, subregions) that have been designated by capital letters (we call it Madmans Alphabet because of the frivolity with which symbols have been introduced and then withdrawn again), and then other loci believed to be associated with the H-2 complex. As in the First Listing (Klein et al. 1978), the core of the review in the Second Listing constitutes the tables of H-2 haplotypes, antigens, and determinants.

Polymorphism of t -complex genes in European wild mice

Thirty-two t haplotypes were extracted from wild mice captured in Central Europe, Spain, the Soviet Union, Israel, Egypt, the Orkneys and South and North America, and tested for lethality in the homozygous state. Twenty-two proved to be homozygous lethals, 8 semilethals and 2 viables. The lethal t haplotypes were then tested by the genetic complementation test for identity with representatives of known complementation groups and with each other. Five of the 22 haplotypes proved to carry previously identified lethality factors ( t w5 , t w73 , and t Lub-1 ), while the rest carried new factors. The 17 haplotypes fell into 8 new complementation groups. Two of the new groups are partially overlapping in that they seem to share some lethality factors and differ in others. These tests raise the total number of known complementation groups to 16. The distribution of the individual t haplotypes among wild mice populations seems to reflect their differentiation from a common ancestor haplotype.

Zebrafish Mhc class II α chain-encoding genes: polymorphism, expression, and function

Its small size and short generation time renders the zebrafish (Brachydanio rerio) an ideal vertebrate for immunological research involving large populations. A prerequisite for this is the identification of the molecules critical for an immune response in this species. In earlier studies, we cloned the zebrafish genes coding for the β chains of the class I and class II major histocompatibility complex (MHc) molecules. Here. we describe the cloning of the zebrafish α chain-encoding class II gene, which represents the first identification of a class II A gene in teleost fishes. The gene, which is less than 3 kilobases (kb) distant from one of the β chain-encoding genes, is approximately 1.2 kb long and consist of four exons interrupted by very short (<200 base pairs) introns. Its organization is similar to that of the mammalian class II A genes, but its sequence differs greatly from the sequence of the latter (36% sequence similarity). Among the most conserved parts is the promoter region, which contains X, Y, and TATA boxes with high sequence similarity to the corresponding mammalian boxes. The observed striking conservation of the promoter region suggests that the regulatory system of the class II genes was established more than 400 million years ago and has, principally, remained the same ever since. Like the DMA, but unlike all other mammalian class II A genes, the zebrafish gene codes for two cysteine residues which might potentially be involved in the formation of a disulfide bond in the α1 domain. The primary transcript of the gene is 1196 nucleotides long and contains 708 bucleotides of coding sequence. The gene is expressed in tissues with a high content of lymphoid/myeloid cells (spleen, pronephros, hepatopancreas, and intestine). The analyzed genomic and cDNA sequences are probably derived from different loci (their overall sequence similarity in the coding region is 73% and their 3′ untranslated regions are highly divergent form each other). The genes are apparently functional. Comparison of genes from different zebrafish populations reveals high exon 2 variability concentrated in positions coding for the putative peptide-binding region. Phylogenetic analysis suggests that the zebrafish class II A genes stem form a different ancestor than the mammalian class II A genes and the recently cloned shark class II gene.

Cloning and characterization of class I Mhc genes of the zebrafish, Brachydanio rerio.

The zebrafish (Brachydanio rerio) offers many advantages for immunological and immunogenetic research and has the potential for becoming one of the most important nonmammalian vertebrate research models. With this in mind, we initiated a systematic study of the zebrafish major histocompatibility complex (Mhc) genes. In this report, we describe the cloning and characteristics of the zebrafish class I A genes coding for the α chains of the αβ heterodimer and thus complete the identification of all four classes and subclasses of the Mhc in this species. We describe the full class I α cDNA sequence as well as the exon-intron organization of the class I A genes, including intron sequences. We identify three families of class I A genes which we designate Bree-UAA,-UBA, and -UCA. The three families originated about the time of the divergence of cyprinid and salmonid fishes. All three families are members of an ancient lineage that diverged from another, older lineage also represented in cyprinid fishes before the radiation of teleost orders. The fish class I A genes therefore evolve differently from mammalian class I A genes, in which the establishment of lineages and families mostly postdates the divergence of orders.

Polymorphism of the HLA class II loci in Siberian populations.

Abstract The populations that colonized Siberia diverged from one another in the Paleolithic and evolved in isolation until today. These populations are therefore a rich source of information about the conditions under which the initial divergence of modern humans occurred. In the present study we used the HLA system, first, to investigate the evolution of the human major histocompatibility complex (MHC) itself, and second, to reveal the relationships among Siberian populations. We determined allelic frequencies at five HLA class II loci (DRB1, DQA1, DQB1, DPA1, and DPB1) in seven Siberian populations (Ket, Evenk, Koryak, Chukchi, Nivkh, Udege, and Siberian Eskimo) by the combination of single-stranded conformational polymorphism and DNA sequencing analysis. We then used the gene frequency data to deduce the HLA class II haplotypes and their frequencies. Despite high polymorphism at four of the five loci, no new alleles could be detected. This finding is consistent with a conserved evolution of human class II MHC genes. We found a high number of HLA class II haplotypes in Siberian populations. More haplotypes have been found in Siberia than in any other population. Some of the haplotypes are shared with non-Siberian populations, but most of them are new, and some represent “forbidden” combinations of DQA1 and DQB1 alleles. We suggest that a set of “public” haplotypes was brought to Siberia with the colonizers but that most of the new haplotypes were generated in Siberia by recombination and are part of a haplotype pool that is turning over rapidly. The allelic frequencies at the DRB1 locus divide the Siberian populations into eastern and central Siberian branches; only the former shows a clear genealogical relationship to Amerinds.

Evolutionary relationships between the t and H-2 haplotypes in the house mouse

Thirty-three mouse strains carrying t haplotypes were typed with a large battery of monoclonal and polyclonal antibodies specific for class I and class II antigens controlled by the H-2 complex. Among these t haplotypes were representatives of the six complementation groups defined previously and of eight new groups defined by us recently. The typing resulted in the identification of the H-2 haplotypes of these strains and of their alleles at K, D, A, and E loci. Nineteen of the 33 strains proved to carry a mutation that prevents the expression of the E molecule on the cell surface. All H-2 haplotypes of the t strains are related in terms of sharing certain antigenic determinants, most of which have not, as yet, been found in inbred strains or in wild mice that do not carry t haplotypes. According to the degree of serological relatedness, the haplotypes can be arranged into a pedigree presumably reflecting the evolutionary history of the t chromosomes. The ancestral t chromosome from which the 33 chromosomes derive was presumably present in the mouse population before the divergence of the Mus musculus and Mus domesticus species. The E° mutation, too, is apparently ancient because it occurs in different branches of the evolutionary tree.

A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish

BackgroundThe genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number of linked genes (e.g. greater than 200 in humans) with predominantly immune function. In some birds, it consists of only a small number of linked MHC core genes (e.g. smaller than 20 in chickens) forming a minimal essential MHC and, in fish, the MHC consists of a so far unknown number of genes including non-linked MHC core genes. Here we report a survey of MHC genes and their paralogues in the zebrafish genome.ResultsUsing sequence similarity searches against the zebrafish draft genome assembly (Zv4, September 2004), 149 putative MHC gene loci and their paralogues have been identified. Of these, 41 map to chromosome 19 while the remaining loci are spread across essentially all chromosomes. Despite the fragmentation, a set of MHC core genes involved in peptide transport, loading and presentation are still found in a single linkage group.ConclusionThe results extend the linkage information of MHC core genes on zebrafish chromosome 19 and show the distribution of the remaining MHC genes and their paralogues to be genome-wide. Although based on a draft genome assembly, this survey demonstrates an essentially fragmented MHC in zebrafish.