DNA sequences near a meiotic recombinational breakpoint within the human HLA-DQ region

MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.

Pseudogenes: are they "junk" or functional DNA?

Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.

Immune related genetic polymorphisms and schizophrenia among the Chinese

Genetic association studies were conducted among two independent cohorts of Chinese ethnicity. The samples consisted of cases and unrelated controls, ascertained from Guangzhou, China, and Singapore. The studies were prompted by our earlier report of an association between schizophrenia and HLA DQB1 alleles (HLA DQB1*0602 and HLA DQB1*0303) in the Singapore sample. Polymorphisms of HLA DQB1 and flanking markers on chromosome 6p21.3 were investigated in the first part of the study. A significant negative association with HLA DQB1*0402 was detected in the Guangzhou sample (Odds ratio, OR 0.26, 95% confidence intervals, CI 0.1, 0.6; p < 0.02, corrected for multiple comparisons). Additional analysis of the Guangzhou and Singapore samples revealed associations at three other anonymous markers flanking HLA DQB1. In the second part of the study, three polymorphisms at the Interleukin-1 gene cluster (IL-1, chromosome 2q13-q21) were investigated in both cohorts, since associations with schizophrenia have been reported in another sample. Persuasive evidence for an association at IL-1 was not detected in either sample. Our results suggest a susceptibility locus for schizophrenia in the HLA region among the Chinese, but further clarification is necessary.

Trans-speciation maintenance in the MHC region of a polymorphism which includes a polymorphic dinucleotide locus, and the de novo arisal of a polymorphic tetranucleotide microsatellite

Alleles and the surrounding regions of DQCAR, a dinucleotide repeat tightly linked to HLA-DQB1, were sequenced in a range of primate species including man. Three polymorphic regions can usefully be defined in the description of these sequences: the dinucleotide GT repeat itself, the anonymous region 5' of this repeat, and a variable CTGT repeat in the 3' region. The 5' sequence displayed six alleles in the individuals studied. One of these alleles was invariably associated with substitutions in the GT repeat and absence of the CTGT repeat, the others with pure, polymorphic GT repeats and variation in the numbers of CTGT repeats. Haplotypes can be classified by the allele in the 5' region. Those carrying allele 1 were only found in man, those with allele 2 in man, chimpanzee and gorilla. The third haplotype (indicated by the presence of allele 3) was found in chimpanzee, gorilla and orang-utan, the fourth in chimpanzee and gibbon, the fifth in baboon, guenon and mangabey and the sixth in guenon and macaque. The alleles in the 5' region, but from different species, are thus often more similar than alleles from the same species, a phenomenon already shown for some HLA genes. This suggests that major histocompatibility sequences and surrounding sequences shared a correlated evolutionary history. The new polymorphic tetranucleotide microsatellite (CTGT, 3rd region) has possibly arisen de novo from the pre-existing dinucleotide GT. This study provides information not only on the molecular evolution of this particular microsatellite but also of the trans-speciation maintenance of polymorphism of its surrounding sequences.

Genome sequencing analysis of the 1.8 Mb entire human MHC class I region

The human MHC class I region spans 1.8 Mb from the MICB gene to the HLA-F gene at the telomeric end of the HLA region. There are fewer genes recognized in this region than in the class II or class III region, probably because this region remained uncharacterized for genomic organization. Based on the 1,796,938 bp genomic sequence of the entire class I region determined in our laboratory, the complete gene structure of this region has finally emerged. This region embraces as many as 118 genes (73 known and 45 new genes) with a gene density of one gene every 15.2 kb, which is comparable to that of the gene-rich class III region. The GC content is fairly uniform throughout the class I region, being 45.8% on average, which corresponds to the isochore H1. By investigation of genetic polymorphisms in 26 out of 758 microsatellite repeats identified in the class I region, we could reduce the critical region for Behçet's disease (associated with B51) and psoriasis vulgaris (associated with Cw6) to approximately 50 kb segments, between MICA and HLA-B and between TCF19 and S, respectively. Thus, systematic large-scale genomic sequencing provides an efficient way of identifying genes and of mapping disease-susceptible genes in the genome.

Recombination within the human MHC

Recombination (crossing over) in the human MHC is thought to have played a role in generation of novel alleles at various HLA loci. It is also responsible for the diversity observed at the haplotype level, although the functional consequences of this activity are not clear. Historic and family studies of recombination have provided estimations of recombination fractions across the MHC and identified potential hotspots for recombination in the class II region. Other characteristics of recombination in the human MHC such as haplotype specificity in recombination frequency and localized sequence motifs involved in recombination have been considered, but have been difficult to address given the constraints of human population studies. Single-sperm typing holds promise in overcoming some of the limitations inherent in the study of recombination in human populations. Both family-based and sperm typing analyses of recombination, along with our knowledge of linkage disequilibrium patterns in the MHC, may provide novel information regarding the evolution of HLA haplotypes that will be difficult to obtain by other means.

Microsatellite single nucleotide polymorphisms in the HLA-DQ region

Sequencing studies were performed in three previously described microsatellite and minisatellite markers located within the HLA-DQ region, DQCAR, DQCARII and G51152. Multiple nucleotide substitutions that did not change size polymorphisms were observed in all three markers. In all loci, the number of core repeats did not correlate with neighboring DQ allele sequence motifs while single nucleotide changes within or flanking the microsatellite sequence did. This result indicates higher mutation rates for microsatellite expansions/contractions than for nucleotide substitutions in these loci. Further analysis indicated an almost complete phylogenetic correspondence between DQCAR single nucleotide polymorphisms (SNPs) and DQB1 sequences on one side (1.0-1.5 kb apart) and a complete relationship between DQCARII and DQA1 sequences on the other (4.5 kb apart). In contrast, G51152 sequences did not correspond perfectly with DQB1 allelic sequences, thus suggesting the existence of several ancestral crossovers between this marker and DQB1 (20-25 kb). Sequencing microsatellites might be useful in disease mapping studies by increasing marker informativeness and by helping in the interpretation of association study results. It is also proposed that SNPs within the flanking region of CA repeats could be used to develop biallelic markers from already available mapped microsatellite markers.

Nucleotide sequencing analysis of the 146-kilobase segment around the IkBL and MICA genes at the centromeric end of the HLA class I region

To elucidate the complete gene structure and to identify new genes involved in the development of HLA class I antigen-associated diseases in the class I region of the human major histocompatibility complex on chromosome 6, a YAC clone (745D12) covering the 146-kb segment around the IkBL and MICA loci was isolated from a YAC library constructed from the B-cell line, BOLETH. A physical map of this region was constructed by isolation of overlapping cosmid clones derived from 745D12. Of these, five contiguous cosmids were chosen for DNA sequencing by the shotgun strategy to give a single contig of 146,601 bp from 2.8 kb telomeric of the IkBL gene to exon 6 of MICA. This region was confirmed to contain five known genes, IkBL, BAT1, MICB, P5-1, and HLA-X (class I fragment), from centromere to telomere, and their exon-intron organizations were determined. The 3.8-1 homologue gene (3.8-1-hom) showing 99.7% identity with the 3.8-1 cDNA clone, which was originally isolated using the 3.8-kb EcoRI fragment between the HLA-54/H and the HLA-G genes, was detected between MICA and MICB and was suggested to represent the cognate 3.8-1 genomic sequence from which the cDNA clone was derived. No evidence for the presence of expressed new genes could be obtained in this region by homology and EST searches or coding and exon prediction analyses. One TA microsatellite repeat spanning 2545 bases with as many as 913 repetitions was found on the centromeric side of the MICA gene and was indicated to be a potential hot spot for genetic recombination. The two segments of approximately 35 kb upstream of the MICA and MICB genes showed high sequence homology (about 85%) to each other, suggesting that segmental genome duplication including the MICA and MICB genes must have occurred during the evolution of the human MHC.

First report of recombination between the HLA-DR and HLA-DQ loci within a family

Although unusual associations of HLA-DR and HLA-DQ alleles seen in ancestral haplotypes have indicated that recombination between these genes occurred in the past, an actual crossover event between DR and DQ has never been shown within a family. In a study of families with Graves' disease we have identified an individual from a three generation family who inherited a maternal haplotype that is the result of a recombinational event between the HLA-DR and the HLA-DQ loci on her chromosomes. Family members were typed for HLA class I by the lymphocyte microcytotoxicity test and for HLA class II by polymerase chain reaction (PCR) with sequence-specific primers or with sequence-specific oligonucleotide probes after PCR. Based on linkage disequilibrium it is likely that the recombinant haplotype is present in the proband rather than his brother. This haplotype was subsequently inherited by one of the proband's sons. The data presented support the conclusion that the recombinant haplotype resulted from a crossover event between the mother's DRB1 and DQA1 genes. Thus, recombination between the HLA-DR and HLA-DQ genes has been demonstrated within this family; a recombination event not previously described.

The complex mutation pattern of a microsatellite

DQCAR is a (CA)n microsatellite located in the HLA class II region and tightly linked to HLA-DQB1. Previous studies showed a strikingly low level of size variation in DQCAR alleles within an extensive subfamily of HLA-DQ subtypes (DQ1). DQCAR alleles in non-DQ1 subtypes showed a higher degree of size polymorphism. In this study sequence analysis demonstrates that DQ1-associated DQCAR alleles have a single C-->A nucleotide substitution interrupting the CA repeat array. Frequent CA-->GA mutations are also observed in DQ1-associated microsatellites with identical allele sizes. In contrast, DQCAR alleles associated with non-DQ1 haplotypes display a perfect CA repeat sequence and the variation in allele size is attributable only to differences in the number of CA repeats. Our results imply that several mutational mechanisms are involved in the generation of allelic diversity within the same microsatellite locus. The possibility of different mutation rates in the same locus should to be taken into account when using these markers in evolutionary and disease studies.

Evidence for individual and between-family variability of the recombination rate in cattle

We have conducted a study based on single sperm typing in a family design to assess patterns of variability of the male recombination rate in cattle. 2214 sperm of 37 bulls were typed for 11 loci on bovine Chromosomes (Chrs) 6, 23, and the sex chromosomes. Statistically significant individual variability of the recombination rate was observed for one interval in the pseudoautosomal region (PAR) of the bovine sex chromosomes; one marker interval on bovine Chr 23 exhibited individual variability that was close to significance. Thirty-five of the bulls were members of six paternal halfsib groups, and highly significant variability between families was found for one interval in the PAR. This variability may be due to DNA sequence differences in the PAR or to a genetic control of the recombination activity in this region. It is demonstrated that differences in the recombination rate of the magnitude observed in the present study may have a considerable impact on the power of QTL mapping experiments as well as on the sustainability of marker-assisted selection strategies.

Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence

The understanding of the mutational mechanism that generates high levels of variation at microsatellite loci lags far behind the application of these genetic markers. A phylogenetic approach was developed to study the pattern and rate of mutations at a dinucleotide microsatellite locus tightly linked to HLA-DQB1 (DQCAR). A random Japanese population (n = 129) and a collection of multiethnic samples (n = 941) were typed at the DQB1 and DQCAR loci. The phylogeny of DQB1 alleles was then reconstructed and DQCAR alleles were superimposed onto the phylogeny. This approach allowed us to group DQCAR alleles that share a common ancestor. The results indicated that the DQCAR mutation rate varies drastically among alleles within this single microsatellite locus. Some DQCAR alleles never mutated during a long period of evolutionary time. Sequencing of representative DQCAR alleles showed that these alleles lost their ability to mutate because of nucleotide substitutions that shorten the length of uninterrupted CA repeat arrays; in contrast, all mutating alleles had relatively longer perfect CA repeat sequences.

Linkage disequilibrium between HLA class II (DR, DQ, DP) and antigen processing (LMP, TAP, DM) genes of the major histocompatibility complex

TAP, LMP and DM genes map within the major histocompatibility complex (MHC) class II region between the DQB1 and DPB1 loci, and are involved in the processing of peptides bound to HLA class I or class II molecules. In order to determine the various linkage disequilibria existing between these genes and HLA class II genes, we have analyzed TAP1, TAP2, LMP2, DMA, DMB, DRB1, DQA1, DQB1 and DPB1 polymorphisms in 162 unrelated healthy Caucasian individuals. Many positive or negative associations were observed between alleles at these loci, such as between DR/DQ and TAP2, DM or LMP, between DP and DMB, and between TAP2 and DM, TAP2 and LMP. Conversely, no linkage disequilibrium was detected between some closely related genes (DR/DQ and TAP1, TAP1 and TAP2, LMP2 and DM), in agreement with the existence of recombination hot spots in this region. Other weak linkage disequilibria are likely to exist in this region. These data allow to define some conserved MHC class II haplotypes including HLA class II and TAP, LMP and DM alleles. Furthermore, the knowledge of such linkage disequilibria is of outstanding importance in order to avoid misinterpretation of the data when studying MHC class II associations with autoimmune diseases.

Extensive polymorphism of a (CA)n microsatellite located in the HLA-DQA1/DQB1 class II region

A highly polymorphic (CA)n microsatellite marker (DQCAR), located between the DQA1 and the DQB1 genes, was characterized in four ethnic groups. Based on length polymorphism, 12 alleles could be defined. The marker is located 1- to 2-kb telomeric to the DQB1 gene and 10 kb centromeric to the DQA1 gene and was shown to be in tight linkage disequilibrium with HLA-DQ. Analysis of the linkage disequilibrium pattern revealed little additional diversity in DQ1-associated haplotypes. Almost all DQ1 subjects examined were DQCAR 103 or DQCAR 107 (13 and 15 CA repeats, respectively). In contrast, significant haplotypic diversity was observed for most DQ2-, DQ3-, and DQ4-associated haplotypes. These haplotypes often had longer allele sizes (DQCAR > 111, more than 17 CA repeats) and more DQCAR alleles per haplotype. These haplotypes also carried DQCAR alleles of different sizes, even though they bore the same DQA1 and DQB1 alleles, and sometimes the same DRB1 allele as well. These results indicate that DQCAR could be a useful marker to better define disease associations with HLA. Our results are also consistent with the hypothesis that CAR alleles with higher numbers of repeats have higher mutation rates and that recombination within the HLA-DR/DQ region is haplotype dependent.

Exonic MHC-DRB polymorphisms and intronic simple repeat sequences: Janus' faces of DNA sequence evolution

The evolution of highly polymorphic gene loci is following routes that cannot be extrapolated from the existing knowledge of single copy genes. In addition, interpreting the evolution of the most polymorphic loci in vertebrates requires a plethora of data from different taxa. We evaluate here the rules for the evolution of Major Histocompatibility Complex (MHC-)DRB genes recently established in humans and other primates on the basis of sequences from several artiodactyl species. MHC genes encode essential molecules for self/altered-self/non-self discrimination in the interaction of the organism with its environment. The necessity to effectively present various different antigens to immunocompetent cells causes positive selection pressure on the variability of these genes in the population. Artiodactyls represent the third mammalian order in which this phenomenon was evidence independently. A further incentive to investigate also the surroundings of MHC-DRB loci was the presence of a particular repetitive sequence stretch in the vicinity of the polymorphic exon--in addition to the evolutionarily old alleles, ancient polymorphisms and the mechanisms for their generation and/or maintenance. Besides their utility for indirect gene diagnosis (MHC-DRB typing), the closely linked stretches of simple repetitive DNA in the neighborhood of the highly polymorphic MHC-DRB genes are also interesting remains of the evolutionary history. Evolutionary development is different in genetically inert intronic DNA compared to the exonic counterparts, despite their close vicinity. The persistence of these simple repeats over nearly 100 million years in one location preserving the same basic motif structure is startling. Indirect evidence is weighed that biological meaning should be considered for these elements. The combined analysis of the polymorphic DRB genes and the (highly variable but persistent) simple repeat stretches deepen our understanding of the complexities within a unique genomic compartment encoding essential molecules for self/non-self differentiation in the interaction of the organism with its environment.

The minimal polymorphism of class II E alpha chains is not due to the functional neutrality of mutations

Given the extensive allelic amino acid sequence polymorphism present in the first domain of A alpha, A beta, and E beta chains and its profound effects on class II function, the minimal polymorphism in the mouse E alpha chain (and in its human homologue DR alpha) is paradox. Two possible explanations for the lack of polymorphism in E alpha are: (1) the E alpha chain plays such a uniquely critical structural/functional role in antigen presentation, T-cell activation, repertoire selection, and/or pairing with E beta or other proteins for expression that it cannot vary, and mutations are selected against; (2) the E alpha chain plays a less significant role than the outer domains of other major histocompatibility complex (MHC) proteins in determining the interactions with processed peptides or with T-cell receptor (TCR), so there is no selective pressure to maintain new mutations. To explore this question we compared the ability of transfectants expressing wild type (wt) E alpha E beta d and mutant E alpha wt E beta d proteins to present peptides and bacterial superantigens to T-cell hybridomas. Mutations at the E alpha amino acid positions 31, 52, and 65&66, to residues that represent allelic alternatives in A alpha chains, significantly reduced activation of peptide-specific T hybridomas, and mutations at 71 sometimes enhanced T-cell stimulation. None of the E alpha mutations reduced, and some enhanced, superantigen stimulation of T-cell hybridomas. These results argue against the hypothesis that E alpha chains are minimally polymorphic because mutations in E alpha are functionally neutral.

Mutations in the retinoblastoma gene and their expression in somatic and tumor cells of patients with hereditary retinoblastoma

Two intragenic deletions (exon 18-19 and exon 24) and two point mutations (one missense mutation in exon 21 and one mutation at splice-donor site for exon 13) were detected in the retinoblastoma gene in somatic and tumor cells of patients with hereditary retinoblastoma. Three mutations were located in a domain essential for binding to oncoproteins encoded by DNA tumor viruses (Hu et al., 1990; Huang et al., 1990). One mutation (deletion of exon 24) was outside this domain but it is in the region essential for binding to transcriptional factor E2F, and for suppression of malignant phenotypes (Qian et al., 1992; Qin et al., 1992). A minisatellite-like sequence and short repeated sequences were located at the breakpoint of the deletion of exon 24, suggesting that two deletions on both sides of the minisatellite-like sequence may be generated by a "DNA slippage and misalignment" mechanism. Upon amplification of cDNA by the polymerase chain reaction, no transcript of gene with frameshift mutation (deletion of exon 24) was detected in skin fibroblasts, while transcripts of genes with missense mutations were detected. The results, in combination with previous reports (Dunn et al., 1989; Hashimoto et al., 1991), suggest the instability of transcripts with a premature stop codon or the suppressed expression of alleles with a premature stop codon in the retinoblastoma gene in somatic cells of hereditary patients.

Genomic structure and function in the MHC

The major histocompatibility complex (MHC) is a fascinating region of the human genome. More is known about this 4 Mb of DNA (0.1% of the genome) on the short arm of chromosome 6 than about any other region of similar size. Among the 80 or so MHC genes found so far are several clusters with related functions in antigen processing and presentation. In addition to its importance in immunology, the MHC is a useful model for investigating gene organization, polymorphism, linkage disequilibrium and recombination. A large number of diseases, many of the autoimmune type, are associated with the region.

Class I gene contraction within the HLA-A subregion of the human MHC

Individuals expressing either the HLA-A24 or the HLA-A23 histocompatibility antigens have been found to possess an HLA-A class I subregion approximately 50 kb smaller in size than those studied from individuals expressing other HLA-A haplotypes. This originally manifested itself as a haplotype-associated size variation in the NotI and MluI megabase fragments observed on pulsed-field electrophoresis gels after blotting and probing with HLA-A subregion-specific genomic probes. The contracted region falls between the HLA-A and the HLA-G class I genes and specifically includes the novel HLA-A-related pseudogene, HLA-H, as well as the adjacent deteriorated class I pseudogene, 7.0 p. The intactness of locus D6S128, defined by probe pMC6.7 located telomeric to the HLA-H gene, demonstrates that the distal rearrangement point falls within a 20-kb stretch of DNA separating HLA-H from pMC6.7. This extends a previous report regarding variation in class I gene number within the human major histocompatibility complex and precisely localizes the genomic residence of sequences that may define a recombination hot spot. Because the size variation maps to a recombinogenic area, its characterization may ultimately reveal important biological information relevant to the events that shaped the organization of the human HLA class I multigene family.