Gene mapping within the T/t complex of the mouse. II. Anomalous position of the H-2 complex in t haplotypes

Naturally occurring t haplotypes are chromosome 17 polymorphisms that suppress genetic recombination in t/+ heterozygotes over a long distance that includes the H-2 complex. There is strong linkage disequilibrium between t haplotypes and H-2 haplotypes; over 20 independently isolated t chromosomes representing eight different complementation groups share only four H-2 haplotypes. Thus t haplotypes and their associated H-2 loci are inherited en bloc as a “supergene” complex, whose frequency is driven in wild mouse populations by their high transmission from male t heterozygotes. This phenomenon must therefore serve as an important regulator of H-2 polymorphisms. Genes within the region of recombination suppression in t haplotypes have been mapped by crossing-over that occurs readily between two different t haplo-types situated in trans, and by this means we show here that the H-2 complex occupies an anomalous position in t haplotypes, mapping proximal to the locus of tf closely flanked by t-lethal mutations.     

A region flanking H-2K is duplicated to a distant site in most mouse t haplotypes

Mouse t haplotypes contain at least one inversion, which encompasses the major histocompatibility complex, relative to their wild-type counterparts. A DNA probe for a single copy sequence which flanks the H-2K region in inbred strains was found to have undergone further rearrangements in the t haplotypes. In most t haplotypes, this sequence is duplicated at a distant site, and the two regions show 1 % recombination. The length of homology shared by the two sites is likely to be at least 10–15 kb. Three different alleles, as defined by restriction fragment length polymorphisms, were found for each of the two sites among different t haplotypes. These may reveal evolutionary relationships among these chromosomes.     

Molecular probes define different regions of the mouse t complex

Four genomic clones obtained from microdissected fragments of the proximal portion of mouse chromosome 17 have been used to identify a series of t-haplotype-specific restriction fragments. Their specificity is defined by presence in eight complete t haplotypes and absence from 18 inbred strains of wild-type mice. Partial t haplotypes contain subsets of the t-specific fragments, and each can be classified according to the t-specific fragments it contains. This is the first molecular evidence that independent partial t haplotypes contain different lengths of t haplotype DNA. Recombination studies indicate that partial t haplotypes suppress recombination in proportion to the extent of t haplotype DNA they contain. Molecular analysis of partial t haplotyes shows that the t-specific fragments map to and thus define different regions of the t complex. Certain regions of t haplotype DNA defined by t-specific restriction fragments can be correlated with loci involved in the control of transmission ratio distortion.     

Genetic structure and origin of t haplotypes of mice, analyzed with H-2 cDNA probes

We investigated the genetic organization and evolutionary origin of t chromosomes of mice by examining the restriction fragment patterns of DNA from t haplotypes and normal chromosomes with cDNA probes to H-2 class I genes. On genomic DNA blots, the restriction fragments containing H-2-related sequences were highly variable among different inbred strains of mice, whereas they were very similar among different t haplotypes even when the t haplotypes carried serologically different H-2 haplotypes. These observations suggest that all t haplotypes have a common origin and are not products of independent mutational events. We also mapped the position of several restriction fragments characteristic of t DNA by using a battery of recombinant t haplotypes, defined with respect to their t-lethal factors and H-2 haplotypes. We thus show that restriction fragments containing H-2-related sequences map to the left of the H-2 class I genes in t chromosomes, a region in which the tw32 b-lethal factor also maps. The cloning of these fragments can be expected to provide an entry for the structural analysis of t DNA.     

Limits of the distal inversion in the t complex of the house mouse: Evidence from linkage disequilibria

The suppression of crossing-over and the consequent linkage disequilibrium of genetic markers within the t complex of the house mouse is caused by two large and two short inversions. The inversions encompass a region that is some 15 centiMorgans (cM) long in the homologous wild-type chromosome. The limits of the proximal inversions are reasonably welldefined, those of the distal inversions much less so. We have recently obtained seven new DNA markers (D17Tu) which in wild-type chromosomes map into the region presumably involved in the distal inversions of the t chromosomes. To find out whether the corresponding loci do indeed reside within the inversions, we have determined their variability among 26 complete and 12 partial t haplotypes. In addition, we also tested the same collection of t haplotypes for their variability at five D17Leh, Hba-ps4, Pim-1, and Crya-1 loci. The results suggest that the distal end of the most distal inversion lies between the loci D17Leh467 and D17Tu26. The proximal end of the large distal inversion was mapped to the region between the D17Tu43 and Hba-ps4 loci, but this assignment is rather ambiguous. The loci Pim-1, Crya-1, and the H-2 complex, which have been mapped between the Hba-sp4 and Grr within the large distal inversion, behave as if they recombine from time to time with their wildtype homologs.     

An unstable family of large DNA elements in the center of the mouse t complex

We have cloned 363 kb (× 10³ bases) from a novel, locally dispersed family of 11 large DNA elements, called T66 elements, within the center of complete mouse t haplotypes. Homologies among individual members of the T66 family are observed along a repeated unit of at least 75 kb in length. Individual T66 homology units are classified into three subfamilies through hybridization studies with a series of diagnostic subfamily-specific probes. The organization and number of elements in wild-type forms of chromosome 17 are very different from those found within t haplotype forms of this chromosome. The number of T66 elements present within individual chromosomes is highly polymorphic among both inbred strains of mice and among independently derived t haplotypes. Wild-type chromosomes have between five and nine T66 elements distributed between two loci that are separated by a genetic distance of at least three map units, whereas t haplotypes have between 9 and 11 T66 elements within a single cluster. Many of the rare recovered products of recombination between a t haplotype and a wild-type form of chromosome 17 have resulted from recombination within or near the T66 regions present on each chromosome. Molecular and genetic data lead to the speculation that portions of individual T66 homology units could be involved in t haplotype effects on sperm differentiation.     

A major testicular cell protein specified by a mouse T/t complex gene.

The technique of two-dimensional gel electrophoresis was used to identify a major testicular cell protein, p63/6.9, which is specified by a gene (p63) within the mouse T/t complex on chromosome 17. A wild-type gene causes the expression of one form of this protein, p63/6.9b. All lethal and semilethal t haplotypes derived from wild mice cause the expression of an apparently identical alternate allelic form of the p63/6.9 protein. This protein, p63/6.9a, represents the first t haplotype-specific molecule to be biochemically identified. A dominant haplotype (T^Hp) acts as a null allele of the p63 gene; this unique behavior provides additional evidence for the interpretation of T^Hp as a deletion within the T/t region of chromosome 17. Limited proteolysis of viable testicular cells causes selective cleavage of the p63/6.9 proteins, relative to other detergent-soluble testicular cell proteins known to be internal. This result strongly suggests that p63/6.9 proteins are located on the cell surface. Qualitative and quantitative estimates indicate that p63/6.9 is one of the most prominent proteins on the testicular cell surface. p63/6.9 is expressed in all other mouse cell types analyzed but at greatly reduced levels. Partial t haplotypes obtained from infrequent recombination events were used to map the p63 gene close to the dominant mutation T and separate from the lethal factors of t haplotypes. A 100% correlation was observed between the expression of p63/6.9a and the genetic presence of the tail interaction factor of t haplotypes. The significance of this correlation in terms of the evolution of t haplotypes among wild mice is discussed.     

Mapping of the Sod-2 locus into the t complex on mouse chromosome 17

A human DNA probe specific for the superoxide dismutase gene was used to identify the corresponding mouse gene. Under the chosen hybridizing conditions, the probe detected DNA fragments most likely carrying the mouse Sod-2 gene. Mapping studies revealed that the Sod-2 gene resides in the proximal inversion of the t complex on mouse chromosome 17. All complete t haplotypes tested showed restriction fragment length polymorphism which is distinct from that found in all wild-type chromosomes tested. The Sod-2 locus maps in the same region as some of the loci that influence segregation of t chromosomes in male gametes. The possibility that the Sod-2 locus is related to some of the t-complex distorter or responder loci is discussed. The data indicate that the human homolog of the mouse t complex has split into two regions, the distal region remaining on the p arm of human chromosome 6, while the proximal region has been transposed to the telomeric region of this chromosome's q arm.     

Recombination between two mouse t haplotypes (t w12 tf) and t Lub-1) : Mapping. of the H-2 complex relative to centromere and tufted (tf) locus

A monoclonal antibody known to recognize the H-2.m3 specificity is shown to react with the class I H-2 product of t ^Lub-1 but not t ^w12 tf mice. This reagent was used to study the segregation of the H-2 complex in the progeny of t ^Lub-1 +/t ^ww12 tf females. The most straightforward interpretation of the results presented here is that these t haplotypes carry an H-2 complex located between the centromere and tufted locus. Possible consequences of such a location with regard to the recombination between t haplotypes and chromosome 17 from laboratory mice are discussed.     

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.     

H-2 antigen variants in a cultured mouse leukemia cell line

We have investigated the effect of immune selection against a single gene product on a cultured mouse Friend leukemia cell line. The clonal cell line used is heterozygous at theH-2 complex and expresses theH-2 ^d andH-2 ^b haplotypes. The genes selected against were theH-2K locus alleles. Variants were obtained after a single-step selection using either antiH-2K^b or anti-H-2K^d serum. The phenotypes of the variants obtained showed an interesting asymmetry between the two haplotypes. Selection against theH 2K ^b allele resulted in the isolation of the two expected types of variant-those that had lost only H-2K^b and those that had lost both H-2K^b and the linked H-2D^b. Selection against H-2K^d yielded, exclusively, variants that had lost both the selected antigen and the linked H-2D^d. None of the variants showed an alteration in expression of antigens intrans configuration. Karyotypic analyses of the variants revealed that all the cells had retained both copies of chromosome 17 present in the wild-type cells. The results suggest that the variants did not emerge through chromosome loss.     

Molecular evidence for the rapid propagation of mouse t haplotypes from a single, recent, ancestral chromosome

Mouse t haplotypes are variant forms of chromosome 17 that exist at high frequencies in worldwide populations of two species of commensal mice. To determine both the relationship of t haplotypes to each other and the species within which they exist, 35 representative t haplotypes were analyzed by means of 10 independent molecular probes, including five DNA clones and five polypeptide spots identified by means of two- dimensional gel electrophoresis. All of the tested haplotypes were found to share restriction fragments and polypeptide spots that are absent in mice carrying wild-type forms of chromosome 17. This observation provides the first direct evidence that all of the known t haplotypes are descendents of a single ancestral chromosome. The absence of variation among t haplotypes could mean that this ancestral chromosome existed relatively recently, in which case it would be necessary to postulate introgressions of t haplotypes across species lines to explain their presence in both Mus domesticus and M. musculus. Alternatively, it is possible that the ancestral chromosome existed prior to the split between M. domesticus and M. musculus and that, by chance, our probes fail to detect polymorphisms that exist among the t haplotypes. A further result of our analysis is the characterization of a partial t haplotype in a wild population of Israeli mice.      

Subdivision of the S region of the mouse major histocompatibility complex by identification of genomic polymorphisms of the class III genes

The S region of the mouse major histocompatibility complex (MHC) encodes the class III proteins, the second (C2) and fourth (C4) components of complement, and factor B. Previously, the assignment of S-region haplotypes was based on analysis of protein polymorphisms. The recent availability of C2, C4, and factor B cDNA probes prompted a search for restriction fragment length polymorphisms which would serve as additional genetic markers for these loci. DNA was isolated from livers of mice of all standard inbred H-2 haplotypes and of haplotypes pz and bs. These DNA samples were digested with restriction endonucleases and analyzed by Southern blot. By the pattern of restriction fragment length polymorphism observed, specific markers have been identified in factor B of haplotypes f, u, z, bs, r, and v, and in C4 of haplotypes b, q,f,j,p,s, pz, r, and v. These genetic markers were used in the analysis of S-region composition in strains B10.TFR5 (H-2 ^ap5) and C3H.LG (H-2 ^dx), and a possible intra-S-region recombinant was revealed in the H-2 ^dxhaplotype. The genetic markers identified here subdivide the S region and will be of value in defining further the composition of the complement gene complex of the mouse MHC.     

The Putative Oncogene Pim-1 in the Mouse: Its Linkage and Variation among t Haplotypes

Pim-1, a putative oncogene involved in T-cell lymphomagenesis, was mapped between the pseudo-alpha globin gene Hba-4ps and the alpha-crystallin gene Crya-1 on mouse chromosome 17 and therefore within the t complex. Pim-1 restriction fragment variants were identified among t haplotypes. Analysis of restriction fragment sizes obtained with 12 endonucleases demonstrated that the Pim-1 genes in some t haplotypes were indistinguishable from the sizes for the Pim-1b allele in BALB/c inbred mice. There are now three genes, Pim-1, Crya-1 and H-2 I-E, that vary among independently derived t haplotypes and that have indistinguishable alleles in t haplotypes and inbred strains. These genes are closely linked within the distal inversion of the t complex. Because it is unlikely that these variants arose independently in t haplotypes and their wild-type homologues, we propose that an exchange of chromosomal segments, probably through double crossingover, was responsible for indistinguishable Pim-1 genes shared by certain t haplotypes and their wild-type homologues. There was, however, no apparent association between variant alleles of these three genes among t haplotypes as would be expected if a single exchange introduced these alleles into t haplotypes. If these variant alleles can be shown to be identical to the wild-type allele, then lack of association suggests that multiple exchanges have occurred during the evolution of the t complex.     

Definitive chromosomal location of the H-2 complex by in situ hybridization to pachytene chromosomes

Chromosome 17 of the mouse carries the H-2 complex and the T/t complex. An understanding of the organization of this region and an accurate genetic map of chromosome 17 would be of great value for both immunologists and developmental biologists. Until now the only maps available have been derived solely from recombinational studies using several translocations, an inherently inaccurate method. We have found the definitive location of the H-2 complex by the use of in situ hybridization. Our results show that both the T/t complex and the H-2 complex map to positions far more distal than the generally accepted map positions. This proves that recombination in Robertsonian chromosomes underestimates physical map distances on chromosome 17.     

The molecular organization of the H-2K region of two t-haplotypes: implications for the evolution of genetic diversity.

The genetic diversity between the t12 and tw5 haplotype chromosomes was studied by analyzing the molecular organization of the H-2K region. Twenty-one cosmid clones spanning over 150 kb of the H-2K region of both t-haplotypes were defined, and high resolution restriction maps were determined. Detailed comparison of the t12 and tw5 restriction maps revealed the following. (i) The H-2K regions of both t-haplotypes retain a very similar molecular organization to that reported for B10, BALB/c and AKR. The nucleotide sequence diversity estimated from restriction site polymorphism is 0.68% between the t12 and tw5 haplotypes; these two t-haplotypes are no more similar to one another than BALB/c is to AKR. (ii) Genetic recombination is strongly implicated in generating H-2 polymorphism. (iii) Genetic polymorphisms, defined as small restriction fragment size differences, are observed at multiple sites along the H-2K region. An Alu-like B2 sequence and BAM5-R homologous sequence were identified as the inserted/deleted DNA segments of two of these sites, suggesting that insertion/deletion of mobile elements is a general mechanism for generating genetic diversity.     

Gene mapping within the T/t complex of the mouse. I. t-lethal genes are nonallelic

The t haplotypes of mouse chromosome 17 are natural polymorphisms in wild populations that contain mutations that affect or control such diverse functions as tail length, embryonic lethality and maturation and function of male germ cells. The major impediment to dissecting the genetics of this complex region has been its unusual property of recombination suppression in heterozygotes with wild-type chromosomes. Recently it was shown that recombination suppression does not occur in heterozygotes containing two different t haplotypes, which suggested that t chromosomes may be mismatched with respect to wild-type but share sequences that permit crossing-over between them. Thus for the first time questions of allelism and map positions of the t-lethal mutations can be addressed. We report here the results of three experiments that analyzed the t^w12 haplotype trans to either t^w5, t^w32 or t^w18. In all cases these lethal mutations were nonallelic to t^w12. These results, together with evidence for functional relatedness, suggest the t-lethals may be a gene family spread out over more than 15 centiMorgans of chromosome 17.     

Genetic analysis of the H-2D region using a new intra-D-region recombinant mouse strain

A rare D-region recombination event which gave rise to the B10.RQDB major histocompatibility complex haplotype has been examined to ascertain the nature of the crossover and to determine which class I genes are present in the new alignment of D-region genes. Serologic analysis have shown that the B10 . RQDB major histocompatibility complex recombinant mouse inherited the H-2Dd gene from the B10.T(6R) parental line and the H-2Db gene from the B10.A(2R) parental line, representing the first example of an intra-D-region crossover resulting from an intercross. Previous molecular genetic analyses of the d and b haplotypes revealed structural diversity in the organization of their D-region gene clusters. Hence, the D region is comprised of five class I genes in the d haplotype and only one in the b haplotype. Because allelic relationships among the various D-region genes are not defined, either a homologous or nonhomologous alignment of genes has generated the RQDB crossover. Therefore, the possibility that all three D-region antigen-presenting molecules (Dd, Ld, and Db) might be encoded by the RQDB haplotype was examined. Fluorescence-activated cell sorter and cytotoxic T lymphocyte analyses revealed no detectable levels of H-2Ld cell-surface expression, confirming earlier studies with antibody-mediated cytotoxicity and immunoprecipitation. Southern blot analysis localized the recombination point to within a 1-kb region at the centromeric end of the H-2Ld gene on the B10 . T(6R) chromosome in a region of high homology to the H-2Db gene on the B10 . A(2R) chromosome. Together, these studies define the D region of the RQDB haplotype as containing the five class I genes: Dd, D2d, D3d, D4d, and Db. In addition to providing insight into rare recombination events in the D region, the B10.RQDB mouse should be a useful tool for exploring the function of D-region genes.     

The dynamic of the t-haplotype in wild populations of the house mouse Mus musculus domesticus in Israel

The t-haplotype, a variant of the proximal part of the mouse chromosome 17, is composed of at least four inversions and is inherited as a single genetic unit. The haplotype causes embryonic mortality or male sterility when homozygous. Genes within the complex are responsible for distortion of Mendelian transmission ratio in males. Thus, the t-haplotype in heterozygous males is transferred to over 95% of the progeny. We examined the dynamic and behavior of the t-haplotype in wild populations of the house mouse in Israel. The Israeli populations show high frequency (15%–20%) of both partial and complete t-carrying mice, supporting the suggestion that the t-complex evolved in the M. domesticus line in the Israeli region. In one population that had the highest frequency of t-carrying individuals, we compared the level of gene diversity between t-carrying and normal mice in the marker’s loci: H-2 locus of the major histocompatibility complex (MHC) on the t-haplotype of chromosome 17, three microsatellites on other chromosomes, and the mitochondrial D-loop. Genetic variability was high in all tested loci in both t and (+) mice. All t mice carried the same chromosome and showed the same H-2 haplotype. While t-carrying mice showed significant H-2 heterozygotes access, (+) mice expressed significant H-2 heterozygote deficiency. There were no differences in the level of gene diversity between t and (+) mice in the other loci. Heterozygosity level at the MHC may be an additional factor in the selective forces balancing the t-haplotype polymorphism.     

An H-2K gene of the t w32mutant at the T/t complex is a close parent of an H-2K qgene

Two recombinant mice have been recovered from the progeny of Ttf/t ^w32+ animals. They have lost the t^w32 lethality factor(s) and gained tufted, presumably from the T chromosome. Southern blot analysis of class I genes of these two new partial t ^PA027 and t ^PA286 haplotypes indicates that they have retained at least part of the major histocompatibility complex of the t ^w32 chromosome (H-2 haplotype H-2 ^w28). We have prepared a phage library of Eco RI-digested DNA from homozygous t ^PA027 animals. Upon screening the library with a cDNA probe specific for H-2K genes, we isolated a class I gene displaying all of the distinctive features of a genuine H-2K gene, and which could thus be defined as an H-2K ^w28 gene. The H-2K ^w28 gene is 92–95% homologous to H-2K ^band H-2K ^dgenes and differs significantly from the other class I genes sequenced so far. Homology with the H-2K ^bsequence reaches nearly 100% in the 3 part of the H-2K ^w28 gene. Moreover, the homology with an H-2K ^qcDNA sequence reaches 99.8%. Several hypotheses can account for the near identity of H-2K ^b, H-2K ^q,and H-2K ^w28 gene sequences: either recombination between H-2 ^w28 and H-2 ^band H-2 ^qsequences occurred before or at the.time the strain was established, or the class I genes of the t ^w32 chromosome and the H-2 ^band H-2 ^qgenes found in inbred strains of mice have separated from each other rather recently.