Considerable haplotypic diversity in the RT1-CE class I gene region of the rat major histocompatibility complex

The major histocompatibility complex (MHC) class I region extending between the Bat1 and Pou5f1 genes shows considerable genomic plasticity in mouse and rhesus macaque but not in human haplotypes. In the rat, this region is known as the RT1-CE region. The recently published rat MHC sequence gave rise to a complete set of class I gene sequences in a single MHC haplotype, namely the RT1ⁿ haplotype of the widely used BN inbred strain. To study the degree of genetic diversity, we compared the RT1-CE region-derived class I genes of the RT1ⁿ haplotype with class I sequences of other rat haplotypes. By using phylogenetic tree analyses, we obtained evidence for extensive presence and absence polymorphisms of single loci and even small subfamilies of class I genes in the rat. Alleles of RT1-CE region class I genes could also be identified, but the rate of allelic nucleotide substitutions appeared rather low, indicating that the diversity in the RT1-CE region is mainly based on genomic plasticity.     

The major histocompatibility complex of the rat,RT 1

Recombinational analysis has shown that the rat MHC,RT1 is divided into two regions:RT1.A, which codes for class I (transplantation) antigens, andRT1.B, which controls the humoral immune response and proliferative response to allogeneic cells as well as the expression of class II (Ia) antigens. Serological and sequence studies suggest that there might be more than one antigen-coding locus within theRT1.A region. Results obtained by sequential immunoprecipitation reveal that both regions code for at least two gene products. By implication, theRT1 complex must therefore harbor at least four loci;RT1.A andD coding for class I glycoproteins (45,000 daltons); andRT1.B andE coding for class II (Ia) glycoproteins (35,000 and 28,000 daltons).     

The major histocompatibility complex of the rat,RT1

The antigenic determinants expressed on RBC and lymphocytes and coded for by the MHC, RT1,of the MNR (RT1 ( m )) rat strain were compared to those of the BN.DA(RT1 ( a )), ALB (RT1 ( b )), and AUG (RT1 ( c )) strains by direct cytotoxicity and absorption analysis with RT1 typing sera, sera produced against MNR cells, and sera produced in MNR responders against cells carrying thea, b, andc haplotype determinants. The results indicate that MNR shares major class I (A) antigens with DA, and major class II (B) determinants with AUG, but that MNR differs from DA and AUG with respect to both classes of determinant. It appears, therefore, that the MNR haplotype does not represent a simple composite of the two other haplotypes,RT1 ( a ) andRT1 ( c ), as reported earlier.     

Genomic organization and sequence of the rat major histocompatibility complex class Ia gene RT1.A u

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X82669     

Physical mapping of theE/C andgrc regions of the rat major histocompatibility complex

 Alignment of class I-hybridizing cosmids from an R21 (A ^l B ^l D ^l E ^u grc ⁺ ) genomic DNA library gave two contigs: one [150 kilobases (kb)] encompassed the E/C region, or a large part thereof, and the other (110 kb) contained the grc region which has genes influencing resistance to chemical carcinogens (rcc), fertility (ft), and growth (dw-3). Amplification of gene sequences in the four cosmids in the E/C region using E ^u -specific and LW2 (RT1.C)-specific primers showed that each cosmid contained both E ^u -like and C-like genes. They are clearly different but closely associated, and they show some variation from the prototypic E (E ^u ) and C (LW2) genes, respectively. Comparison of DNA from grc ⁺ and grc ^– strains of rats showed that the deletion in the grc ^– strains was approximately 50 kb, and that it was located on two of the three cosmids in the grc-region contig. The use of specific class I probes showed that the grc region contained tandemly duplicated RT1.O-RT1.N genes and that the RT.BM1 loci lay outside of the grc region. Neither contig reacted with probes specific for class II, TNFA, Hsp70, or RT1.M genes. The data presented here and the previous data in the literature (summarized in Gill et al. 1995) suggest that the gene order in the major histocompatibility complex (MHC) and MHC-linked region of the rat is: A-E/C-grc-M. Received: 6 November 1995 / Revised: 24 January 1996     

Physical mapping of the major histocompatibility complex class II and class III regions of the rat

A contig of overlapping bacterial and P1-derived artificial chromosome (BAC, PAC) clones derived from the inbred rat strain BN was constructed that encompasses the class II and the class III regions of the rat MHC (RT1 complex). The genomic structure of the rat, human, and mouse class II and class III regions is highly similar. However, different from human and mouse, a copy of the C4, Cyp21, and Stk19 genes is found that maps to the class II region in the rat. Gene trees constructed from human, rat, and mouse C4, Cyp21, and Stk19 sequences show species-specific clustering of the duplicated genes. The class II/III contig reported here links two previously published PAC contigs of the BN rat that contain the centromeric and the telomeric class I regions, RT1-A and RT1-C/E/M, respectively. Thus, the MHC of the rat is now completely mapped in a single contig of BAC/PAC clones derived from a single RT1 haplotype and encompasses about 3.7 Mb.     

Physical and genetic mapping of the telomeric major histocompatibility complex region in man and relevance to the primary hemochromatosis gene (HFE).

We performed pulsed-field gel electrophoresis (PFGE) on genomic DNA from a radiation hybrid (RH) cell line and constructed a high-resolution physical map of the major histocompatibility complex class I region in 6p21.3, where the gene for primary hemochromatosis (HFE) is believed to be located. Due to the intact microsegment of hemizygous human genomic DNA preserved in the RH cell line, simplified and distinct restriction fragment banding patterns were generated. Using the RH cell line, we were able to extend the physical map of the HLA class I region to about 3000 kb, order the known HLA class I genes from centromere to telomere: HLA-B, -C, -E, (-A, -H, -G), and -F, and orient the HLA-F gene along the chromosome. The proximity of HLA-F to HLA-A was confirmed by linkage and linkage disequilibrium analysis. This study shows that RH cell lines can be useful for constructing long-range physical maps in specific regions of the human genome with PFGE. Physical and genetic mapping studies of this region are consistent with a localization of the HFE gene proximal or distal to HLA-A.     

Polymorphism and mapping of the class II genes in the rat: RT1.B,RT1.D,and RT1.H,a new DP-like region

The major histocompatibility complex of the rat (RTI) encodes the class II molecules involved with antigen presentation and cell to cell communication. The organization of these class II genes has been studied by Southern blot hybridization using genomic DNA from inbred and recombinant rat strains digested with various restriction endonuclease and hybridized under stringent conditions with probes for mouse class II and human class II genes. Analysis of the restriction fragment length polymorphisms has mapped the class II genes relative to each other. We have confirmed the order of the - and -chain genes in the RT1.B region, mapped the RT1.D region relative to RT1.B and showed that it has - and -chain loci, and identified a new HLA-DP-like locus, RT1.H, to the RT1.A side of RT1. B. The RT1. H and RT1.H genes map to the region around the recombination point in R22, and there appears to be a hot spot of recombination in RT1.H. The H and D genes have high levels of polymorphism; B , B ,and H have intermediate levels of polymorphism, and D has a low level of polymorphism.     

Linkage mapping and physical localization of the major histocompatibility complex region of the marsupial Monodelphis domestica

We used genetic linkage mapping and fluorescence in situ hybridization (FISH) to conduct the first analysis of genic organization and chromosome localization of the major histocompatibility complex (MHC) of a marsupial, the gray, short-tailed opossum Monodelphis domestica. Family based linkage analyses of two M. domestica MHC Class I genes (UA1, UG) and three MHC Class II genes (DAB, DMA, and DMB) revealed that these genes were tightly linked and positioned in the central region of linkage group 3 (LG3). This cluster of MHC genes was physically mapped to the centromeric region of chromosome 2q by FISH using a BAC clone containing the UA1 gene. An interesting finding from the linkage analyses is that sex-specific recombination rates were virtually identical within the MHC region. This stands in stark contrast to the genome-wide situation, wherein males exhibit approximately twice as much recombination as females, and could have evolutionary implications for maintaining equality between males and females in the ability to generate haplotype diversity in this region. These analyses also showed that three non-MHC genes that flank the MHC region on human chromosome 6, myelin oligodendrocyte glycoprotein (MOG), bone morphogenetic protein 6 (BMP6), and prolactin (PRL), are split among two separate linkage groups (chromosomes) in M. domestica. Comparative analysis with eight other vertebrate species suggests strong conservation of the BMP6-PRL synteny among birds and mammals, although the BMP6-PRL-MHC-ME1 synteny is not conserved.     

Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions

 We present the cloning, structural analysis, and mapping of new members belonging to two multigenic families, the B30-RING finger family and the B7.1-B7.2 family, as well as two genes derived by exon shuffling from members of these families. Eight new members were found and three of them map to the human major histocompatibilitiy complex (MHC) region. Phylogenic and physical mapping analysis allowed us to decipher the evolutionary story of these two multigenic families and to shed light on the evolution of the MHC region. We also show that a deductive analysis can be used to predict the existence of a given gene. Received: 17 February 1997 / Revised: 17 March 1997     

Characterization of a class Ib gene of the rat major histocompatibility complex

The cDNA and a partial genomic sequence of a rat class I major histocompatibility (RT1) gene, 11/3R, is reported here. The sequence contains several unique amino acid residues at certain positions, mutations in exon 7 (which is not expressed), a mutation of the canonical exon 8 stop codon to a sense codon, and includes a long 3 unstranslated region (utr). The structure of exon 7 differs from that found in most rat class I genes and resembles exon 7 of most H-2K,D,L.Q genes. Parts of the 3 noncoding region are homologous to the RT1.A-4 and certain H-2 genes. Expression is detectable by northern blot analysis in mitogen-stimulated lymphocytes only, by polymerase chain reaction (PCR) in each tissue tested. After transfection into L cells 11/3R can be shown to be expressible at the cell surface. Probes derived from the 3 noncoding part crosshybridize with a number of restriction fragments which map to the RT1.C region, thus defining a subfamily of RT1.C region genes. Several members of this subfamily are deleted in the M1 RT1 mutant. The 11/3R gene presents typical features of a class Ib gene. Aspects of evolution and the potential of the gene are discussed.The nucleotide sequence data reported in this paper have been submitted to the GenBank molecule sequence data base and have been assigned the accession numbers X67503 ande X67504.