Low H-2 polymorphism in some Israeli wild mouse populations

Two populations of the wild house mouse, Mus domesticus, found living close to each other (one inhabited a chicken coop and the other an open field at the Educational Farm of the Hebrew University of Jerusalem, East Talpiot, Jerusalem) were studied for their H-2 polymorphism. These two populations were selected because they are well characterized in terms of their ecological parameters; they have been under continuous surveillance for several years. Twenty-seven H-2 homozygous lines were produced by mating wild mice from these two populations with laboratory strains. The H-2 ^w homozygotes were then characterized by serological typing with monoclonal and polyclonal antibodies specific for the known allomorphs controlled by the class I H-2K and H-2D loci or the class II H-2A and H-2E loci. They were also used as donors for immunizations and for the selection of antisera defining the H-2 haplotypes carried by these lines. Four new H-2 haplotypes could be identified: H-2 ^w82 (K ^wl6 D^ws2) H-2 ^w83 (K ^w83 D^w16) H-2 ^w84 (K ^w84 D^w84) and H-2 ^w85 (K ^w83D^w84) the last haplotype being a recombinant derived from H-2 ^w83 and H-2 ^w84. Antinsera defining the new haplotypes were then used for a study of the wild populations. This study revealed that the populations contain only the four identified H-2 haplotypes, having three alleles at the H-2K locus (K ^w16 K^w83, K^w84) and three alleles at the H-2D locus (D ^w16, D^w82 and D ^w84). The alleles occur in the populations with a frequency of 0.12–0.54. There were no significant differences in gene frequencies between the two populations, and the allele frequencies remained more or less stable. There was a significant excess of heterozygotes for at least some of the genes, compared with the frequency expected from Hardy-Weinberg equilibrium. The same antisera were also used to type other populations in the vicinity of Jerusalem. In one population, located 30 km west of Jerusalem, the mice failed to react with any of the reagents. In the other two populations, located 15 km west and 40 km northeast of Jerusalem, three of the four H-2 haplotypes found in East Talpiot were present at high frequencies. It appears, therefore, that only three main H-2 haplotypes and two or three minor ones are present in the area around Jerusalem. This study thus provides the first example of a large mainland population in which the H-2 polymorphism is comparable to that of many other non-H-2 loci.     

Intracellular localization of the HLA class II gene products in transfected mouse L cells.

To investigate the impaired cell surface expression of human major histocompatibility antigen (HLA) in transfected L cells, we examined their intracellular localization by immunocytochemistry. HLA class II molecules produced in transfected L cells were mainly detected in the intracellular vesicles and in the nuclear envelope as granular precipitates. The results suggest that the intracellular transport of the newly synthesized molecules in transfected L cells is impaired at some point along the pathway from the rough endoplasmic reticulum (RER) to the medial-, trans-Golgi apparatus.     

Early endosomal maturation of MHC class II molecules independently of cysteine proteases and H-2DM

Major histocompatibility complex (MHC) class II molecules bind and present to CD4(+) T cells peptides derived from endocytosed antigens. Class II molecules associate in the endoplasmic reticulum with invariant chain (Ii), which (i) mediates the delivery of the class II-Ii complexes into the endocytic compartments where the antigenic peptides are generated; and (ii) blocks the peptide-binding site of the class II molecules until they reach their destination. Once there, Ii must be removed to allow peptide binding. The bulk of Ii-class II complexes reach late endocytic compartments where Ii is eliminated in a reaction in which the cysteine protease cathepsin S and the accessory molecule H-2DM play an essential role. Here, we here show that Ii is also eliminated in early endosomal compartments without the intervention of cysteine proteases or H-2DM. The Ii-free class II molecules generated by this alternative mechanism first bind high molecular weight polypeptides and then mature into peptide-loaded complexes.     

Isolation and analysis of H-2 and Ia alloantigens from wild mouse strains.

Immunoprecipitation and SDS-PAGE analysis were used to examine H-2 and Ia antigens from mouse strains with wild-derived MHC haplotypes. Antisera raised against the wild-derived strains contained anti-H-2 and anti-Ia antibodies which precipitated antigen molecules readily distinguishable by a single assay procedure. The antibodies to wild strains were cross-reactive with standard laboratory haplotypes. Evidence supporting the similar genetic organization of wild and standard haplotypes was found, including isolation of separate H-2K and H-2D molecules from a wild-derived strain, and isolation of two separate Ia molecules from a wild-derived strain.     

Intra-H-2 recombination in the mouse. III. I-Region characterization of haplotypes H-2at2, H-2at3 and H-2a2

Serological characterization of three K-S interval recombinant strains, TBR2 (H-2at2), TBR3 (H-2at3) and AIR 1 (H-2a2) was performed using anti-H-2, Ia, Ss and Slp antisera. The data presented here reveal that the crossover events in both TBR2 and TBR3 occurred between the I-A and I-E subregions. In both cases, the H-2K and I-A subregions were derived fron the H-2t1 of chromosome, while the I-E, S and H-2D regions were derived from the H-2b chromosome (KsAkEbSbDb). The H-2a2 chromosome resulted from a crossover event between the H-2a1 and H-2i9 chromosomes. Ia and Ss typing of AIR 1 suggested that the K to I-E regions originated from H-2a1 and the S and D regions originated from H-2i9 (KkAkEkSbDd).     

On naming H2 haplotypes: functional significance of MHC class Ib alleles

George D. Snell began defining and naming the H2 haplotypes many years ago by histogenetic typing. Since then, a few haplotypes have been given an additional letter, such as bc for strain 129, to show that they are minor variants from the prototype (b). But by and large, differences in nonclassical class I antigens have been known (only?) to those in the field without being acknowledged by a separate haplotype symbol. Thus, strains BALB/c and NZB/BlNJ are both considered H2 ^d and strains C3H/HeJ and B10.BR are both called H2 ^k, although each pair differs in the TL and Qa1 antigens. In parallel with the interest in nonclassical class I antigens, the need for an appropriate haplotype nomenclature is growing. The haplotypes that require splitting are b, d, k, q, and s; the symbol bc should be retained and used, and, for the other haplotypes, the suffix 2 denotes a Qa1 ^a haplotype with highly TL-positive thymocytes.     

Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38

Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.     

Gene transfer of H-2 class II genes: antigen presentation by mouse fibroblast and hamster B-cell lines

We have transferred the mouse Ak alpha and Ak beta genes, which encode the class II I-Ak molecule, into mouse L-cell fibroblasts and hamster B cells. I-Ak molecules are expressed on the surface of both cell types. The L-cell and hamster B-cell I-Ak molecules appear normal by serological analyses and two-dimensional gel electrophoresis. Furthermore, the I-Ak molecules on L cells can act as targets for the allogenic T-cell killing of the transformed L cells. The I-Ak molecules in both mouse fibroblasts and hamster B cells can present certain antigens to T-cell helper hybridomas. Thus only class II molecules are required to convert the nonantigen-presenting cell. Accordingly, it will be possible to dissect the structure-function relationships existing between Ia molecules, foreign antigen, and T-cell receptor molecules by in vitro site-directed mutagenesis and gene transfer.     

Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations

ABSTRACT: BACKGROUND: Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials of AIMs, are useful for classifying individuals from distinct continental origins but cannot discriminate individuals with subtle genetic differences from closely related ancestral lineages. Proof-of-principle studies have shown that gene expression (GE) also is a heritable human variation that exhibits differential intensity distributions among ethnic groups. GE supplies ethnic information supplemental to SNPs; this motivated us to integrate SNP and GE markers to construct AIM panels with a reduced number of required markers and provide high accuracy in ancestry inference. Few studies in the literature have considered GE in this aspect, and none have integrated SNP and GE markers to aid classification of samples from closely related ethnic populations. RESULTS: We integrated a forward variable selection procedure into flexible discriminant analysis to identify key SNP and/or GE markers with the highest cross-validation prediction accuracy. By analyzing genome-wide SNP and/or GE markers in 210 independent samples from four ethnic groups in the HapMap II Project, we found that average testing accuracies for a majority of classification analyses were quite high, except for SNP-only analyses that were performed to discern study samples containing individuals from two close Asian populations. The average testing accuracies ranged from 0.53 to 0.79 for SNP-only analyses and increased to around 0.90 when GE markers were integrated together with SNP markers for the classification of samples from closely related Asian populations. Compared to GE-only analyses, integrative analyses of SNP and GE markers showed comparable testing accuracies and a reduced number of selected markers in AIM panels. CONCLUSIONS: Integrative analysis of SNP and GE markers provides high-accuracy and/or cost-effective classification results for assigning samples from closely related or distantly related ancestral lineages to their original ancestral populations. User-friendly BIASLESS (Biomarkers Identification and Samples Subdivision) software was developed as an efficient tool for selecting key SNP and/or GE markers and then building models for sample subdivision. BIASLESS was programmed in R and R-GUI and is available online at http://www.stat.sinica.edu.tw/hsinchou/genetics/prediction/BIASLESS.htm.     

Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans

Genome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation rates should remove signatures of older events. We assess this concept here in a large-scale study. We have analyzed two population pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M. m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of neutral expectation. For eight loci from each population pair we have determined the size of the potential sweep window and applied a second statistical procedure (linked locus statistics). For the two population pairs, we find five and four significant sweep loci, respectively, with an average estimated window size of 120 kb. On the basis of the analysis of individual allele frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of 400–600 years ago. Given the known population history for the French–German population pair, we infer that the average frequency of selective sweeps in these populations is higher than 1 in 100 generations across the whole genome. We discuss the implications for adaptation processes in natural populations.     

The histocompatibility-2 system in wild mice. XI. Ss and Slp properties of wild-derived H-2 haplotypes

In this study, 14 B10.W lines were examined for genetic traits associated with the Ss protein and Slp alloantigen. Three B10.W lines were found to possess low levels of serum Slp alloantigen. Of these three Slp-positive lines, expression of the alloantigen was sex-limited in two lines (B10.LIB55 and B10.STA12) and constitutive, i.e., found in both sexes, in the remaining line (B10.KPB128). Lines which were found to be Slp-negative were also tested for IA-controlled immune response to Slp alloimmunization. The finding that one of these Slp-negative lines produced no detectable anti-Slp indicates that nonresponder alleles exist in wild populations. Further, the discovery of an unexpected immune response to Slp in F1 hybrids involving lines B10.LIB55 and B10.STA12 suggests the existence of a variant form of Slp alloantigen in these lines.     

Interaction of monoclonal antibodies with MHC class I antigens on mouse spleen cells. II. Levels of expression of H-2K, H-2D, and H-2L in different mouse strains

The numbers of MHC class I molecules expressed by spleen cells from various mouse strains were determined by using MHC-specific monoclonal antibodies and a radioactive binding assay. Although small differences were found to exist in some cases, our general conclusion is that different mice of the same strain, congenic mice of different haplotypes, and syngeneic mice of varying background all express similar numbers of class I antigens. B10.A mice (8 to 10 wk old), for example, express 5.3 X 10(4) Kk molecules/cell, 5.4 X 10(4) Dd molecules/cell, and 2.2 X 10(4) Ld molecules/cell. Some of the differences observed in class I antigen expression included: 1) the level of Kk expression increased to a small but significant extent with age in B10.A mice; 2) female B10.A mice expressed slightly higher amounts of Kk than male mice; and 3) B10.A(2R) and B10.A(4R) recombinant strains expressed elevated levels of K-end antigens and slightly decreased levels of D-end antigens when compared with the unrecombinant B10.A strain. In several strains, F1 mice express approximately 50% as many copies of each parental antigen as do the homozygous parents. B10 mice, which are negative for the L antigen, nevertheless express the same total number of D-end molecules as do B10.A mice. The data suggest that the levels of expression of MHC class I molecules are controlled by at least two factors: gene dosage and another factor(s) that gives rise to the small variations in class I antigen expression seen with age, sex, and strain, and to the low expression of Ld relative to Dd and Kk.     

H2-restricted recognition of cloned HLA class I gene products expressed in mouse cells

Long-term syngeneic mouse cytolytic T lymphocyte (CTL) clones were obtained from DBA/2 (H2d) mice immunized with P815 (H2d) cells transfected with cloned human class I histocompatibility genes, HLA-CW3 or HLA-A24. Three distinct patterns of specificity were defined on P815 HLA transfectant target cells. One clone lysed HLA-CW3 but not -A24 transfectants, and a second lysed HLA-A24 but not -CW3 transfectant target cells. The third clone lysed P815 targets transfected with either HLA gene. None of the CTL clones lysed L cells (H2k) transfected with the same HLA genes or human targets that expressed these HLA specificities. Several lines of evidence indicated that recognition of HLA transfectants by these CTL clones was H2 restricted. First, lysis of P815 HLA transfectants could be inhibited by anti-H2Kd monoclonal antibody. In addition, the anti-P815-HLA CTL clones could lyse a (human X mouse) hybrid target that expressed both HLA class I and H2Kd antigens, but not a clonal derivative that no longer expressed H2Kd. The most direct evidence for H2-restricted recognition of P815-HLA transfectants by the syngeneic CTL clones was obtained by double transfection of mouse L cells (H2k) with both HLA and H2 class I genes. L cells transfected with HLA and H2Kd genes were susceptible to lysis by the same CTL clones that lysed the corresponding P815-HLA transfectant targets. Thus under certain conditions, CTL recognition of xenogeneic class I histocompatibility gene products can be restricted by other class I gene products.     

Effect of Y chromosome and H-2 complex derived from Japanese wild mouse on sperm morphology

Segregation of sperm abnormality level and H-2 haplotypes was investigated in F2 hybrid males obtained from reciprocal crosses involving two B10.congenic strains carrying H-2 and the Y chromosome of Japanese wild mice: B10.MOL-OHM (H-2wm4, 23.1% of sperm abnormalities) and B10.MOL-OKB (H-2wm8, 11.1% of sperm abnormalities). In both types of crosses mean levels of abnormal spermatozoa were significantly higher for males typed as H-2wm4/H-2wm4 than for heterozygous H-2wm4/H-2wm8 or homozygous H-2wm8/H-2wm8. These results suggest that the gene for high sperm abnormality is linked to H-2 complex of the B10.MOL-OHM strain.     

Evolution of HLA class II molecules: Allelic and amino acid site variability across populations

Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations.