Evolutionary evidence of the effect of rare variants on disease etiology.

The common disease/common variant hypothesis has been popular for describing the genetic architecture of common human diseases for several years. According to the originally stated hypothesis, one or a few common genetic variants with a large effect size control the risk of common diseases. A growing body of evidence, however, suggests that rare single-nucleotide polymorphisms (SNPs), i.e. those with a minor allele frequency of less than 5%, are also an important component of the genetic architecture of common human diseases. In this study, we analyzed the relevance of rare SNPs to the risk of common diseases from an evolutionary perspective and found that rare SNPs are more likely than common SNPs to be functional and tend to have a stronger effect size than do common SNPs. This observation, and the fact that most of the SNPs in the human genome are rare, suggests that rare SNPs are a crucial element of the genetic architecture of common human diseases. We propose that the next generation of genomic studies should focus on analyzing rare SNPs. Further, targeting patients with a family history of the disease, an extreme phenotype, or early disease onset may facilitate the detection of risk-associated rare SNPs.

Staggered clines in a hybrid zone between two chromosome races of the harvestman Gagrellopsis nodulifera (Arachnida: Opiliones).

We analyzed a hybrid zone between two chromosome races (2n = 16 and 2n = 22) of a Japanese harvestman, Gagrellopsis nodulifera Sato and Suzuki (Arachnida: Opiliones: Phalangiidae). The hybrid zone is located in the eastern part of Tottori Prefecture, western Honshu. The width of the zone is approximately 5 to 15 km. Three independent tandem fusions/fissions seem to be the main cause of the karyotypic differences between the parental races. Ten karyotypic variants were found in the hybrid zone. They differed by numbers of diploid chromosomes and trivalents detected in meiosis. In most of the collecting sites, karyotypic heterozygotes were less common than expected. A positive correlation was found between number of trivalents in a karyotype and its deficiency rate. In some sites, the deficit of heterozygous individuals was accompanied by an excess of the intermediate homozygotes. One of the three transects across the zone was studied in detail. We found that three types of single heterozygotes (2n = 17, 2n = 19 and 2n = 21) formed a series of successive, spatially separated peaks along the transect. Two types of intermediate homozygotes (2n = 18 and 2n = 20) were also spatially separated. The most parsimonious explanation of such a structure is the staggering of clines of three tandem (or Robertsonian) fusion/fission variants that differentiate the parental races caused by selection against multiple heterozygotes. Analysis of nondisjunction in single heterozygotes demonstrated that there was a strong interindividual variation in nondisjunction rate. The mean frequency of aneuploid MII in single heterozygotes was 0.10 +/- 0.03. Crossover exchanges in some critical regions of trivalents result in abnormal chromosomal configurations: chromosomes with unequal chromatids and dicentric chromosomes. Frequency of crossover-induced chromosomal abnormalities was low in single heterozygotes (approximately equal to 4%), and was unexpectedly high in the double heterozygotes (approximately equal to 15%). Selection against karyotypic heterozygotes is considered as a main evolutionary force responsible for the structuring of the hybrid zone. A positive association between diploid chromosome number and altitude was found. The race 2n = 16 tended to occupy lower altitudes than the 2n = 22 parental race. Differences in ecological preferences may be a result of previous adaptations to different environments in allopatry. A hypothesis concerning the origin and evolution of the hybrid zone is proposed.

Morphology and Meiotic/Mitotic Behavior of B Cromosomes in a Japanese Harvestman, Metagagrella tenuipes (Arachnida: Opiliones): No Evidence for B Accumulation Mechanisms.

Earlier, it has been demonstrated that wild populations of a Japanese harvestman Metagagrella tenuipes (Arachnida: Opiliones) are polymorphic for B chromosomes. In this paper, we present results of a study of the morphology and mitotic and meiotic behavior of the Bs. The B chromosomes varied considerably in size and proportion of eu- and heterochromatin. The single nucleolus organizing region, found in males, was located on a chromosome of the A complement. Some intercell variation in number of Bs may be explained by accidental chromosome losses during chromosome preparation. We also found no intertissue variation in number of Bs. There were also no differences in mean number of B chromosomes per individual among males and females, adult and subadult harvestmen. Segregation of Bs in mitotic and meiotic divisions was nonrandom; B chromosomes tended to segregate equally between daughter cells. The results obtained provide no support for the hypothesis of existence of B accumulation mechanism in this species.

[Cytogenetic study of synapsis and crossing-over in male mice heterozygous for reciprocal translocation T(14; 15)6Ca]. / Tsitogeneticheskoe issledovanie sinapsisa i krossingovera u samtsov myshei, geterozigotnykh po retsiproknoi translokatsii T(14; 15)6Ca.

Synapsis and crossing over in male mice heterozygous for reciprocal translocation T (14; 15)6Ca were studied. The translocated multivalent undergoes the synaptic adjustment in the course of meiotic prophase. Translocated distal region of the 14th chromosome forms inproportionally long lateral element of synaptonemal complex. The number of chiasmata in the 14th chromosome increases from 1.02 0.02 in normal karyotype to 1.41 0.03 in heterozygous mice. The density of chiasmata in translocated, distal region is ten times higher than in the other part of the 14th chromosome.

[Distribution of chiasmas in the 2d and 6th chromosomes involved in Robertsonian translocations in male mice]. / Analiz raspredeleniia khiazm u samtsov myshei po 2-oi i 6-oi khromosomam, vovlechennym v robertsonovskie cliianiia.

The distribution of chiasmata in 2 and 6 chromosomes in males homozygous for Rb(2.6)4Iem and Rb(8.17)1Iem was studied. Chiasmata were shown to distribute along chromosomes non-randomly, exchanges occurring in telomeric regions. Chiasmata distribution is substantially different for the cases of one and two chiasmata per bivalent. The main cause for these differences is supposed to be strong positive chiasmata interference (the position of the first chiasma may determine the position of the second one). The centromere blocks this effect, so chiasma in one arm does not interfere with that in the second arm. It has been shown that the frequency of double exchanges depended on not only the distance between markers under study, but also on marker position in the chromosome.

[Chiasmata distribution in the normal karyotype of mice]. / Raspredelenie khiazm v normal'nom kariotipe myshi.

The number of chiasmata per cell and variance of chiasmata numbers were studied, as well as the recombinational interaction between different bivalents in CBA/Lac mice male line. No competition of bivalents for chiasmata was discovered in mice; at the same time, the chiasmata within one arm of the chromosome interfere with each other. The number of chiasmata per bivalent is estimated for each chromosome independently. The number of chiasmata per chromosome is limited both from below (minimum one chiasma independently of its size) and from above (positive interference of chiasmata).

[Cytogenetic consequences of hybridization between wild and laboratory mice]. / Tsitogeneticheskie posledstviia gibridizatsii mezhdu dikimi i laboratornymi myshami.

Wild mice from the aboriginal population were crossed with the laboratory C57BL/6 mice. F1 hybrids were backcrossed with both parents. Significant increase of recombination frequency in the AY-Ra region of the 2nd chromosome (from 22.0 to 33.1 cM), of the frequency of occurrence of X-Y univalents (up to 54.6%) and of autosomal univalents (up to 9.1%) was found in the F1. In backcrosses all these induces decreased gradually.

[Effect of emotional stress on the frequency of meiotic abnormalities in male mice]. / Vliianie émotsional'nogo stressa na chastotu meioticheskikh narushenii u samtsov myshei.

The effect of stress on the recombination frequencies at the 1st and 2nd chromosomes of male mice was shown earlier. The purpose of this work is the study of the stress effects on the behaviour of meiotic chromosomes. Male mice (A/He and DD/J inbred strains) were treated with acute immobilizing stress at different periods, prior to killing. It was shown that the stress significantly increases the frequency of X-Y and autosomal univalents in metaphase 1 and aneuploidy in metaphase 2. The most sensitive to the stress are the late interphase - early leptotene cells.

[Variation in the relative length of chromosomes in mammalian karyotypes. Hypothesis of equalizing selection]. / Izmenchivost' otnositel'nykh dlin khromosom v kariotipakh mlekopitaiushchikh. Gipoteza vyravnivaiushchego otbora.

A hypothesis on the selective neutrality of relative lengths of karyotype chromosomes was tested. Idiograms expected based on an assumption of selective neutrality of chromosome lengths were compared with actual idiograms in more than a hundred mammalian species. The observed idiograms differed from those expected in a similar manner: in the observed idiograms, the longest chromosomes were shorter, and the shortest were longer than expected. It is suggested that karyotype chromosome variation is limited by selection against chromosome rearrangements that produce very long or very short chromosomes. An analysis of reciprocal translocations in the mouse and Drosophila showed that translocations generating chromosomes of extreme lengths were more deleterious than those generating normal-sized chromosomes. A working hypothesis was advanced stating that within-karyotype variation of chromosome lengths is accounted for by two factors: chromosome rearrangements and natural selection. Chromosome rearrangements tend to randomize relative chromosome lengths in a karyotype, whereas natural selection acts to equalize them.

[Cytogenetic analysis of recombination interactions]. / Tsitogeneticheskii analiz rekombinatsionnykh vzaimodeistvii.

Chiasma interference between separate regions of chromosomes was studied in three phylogenetically distant species. All these species displayed the similar patterns of chiasma interference. Chiasma completely suppressed recombination in the regions next to chiasma within a chromosome's arm. The level of crossing-over suppression decreased non-linearly with increase in a distance between the chiasma and the region under analysis. Some kind of the threshold effect was observed. In some cases, negative interference between the regions rather remote from each other was noted. Polarity of interference was revealed: interstitial chiasma suppressed recombination in the proximal (in relation to the centromere) direction more effectively than in the distal direction. Some regions belonging to the different arms of the same chromosome were shown to be able to interfere.

[Synapsis and recombination of chromosomes in the house mouse homozygous for the double inversion of the homogeneously stained regions in chromosome 1]. / Sinapsis i rekombinatsiia khromosom u gomozigot po dvoinoi inversii gomogenno okrashivaemykh raionov v 1-i khromosome domovoi myshi.

Examination of the meiotic pattern of chromosome 1 isolated from feral mouse population and containing a double insertion (Is) of homogeneously staining regions (HSRs) was carried out. In the previous study it has been shown that the region delineated by the proximal break point of Is(HSR; 1C5) 1Icg and the distal one of Is(HSR; 1E3) 2Icg is desynapsed during early pachytene and heterosynapsed at midpachytene. No synaptic disturbances were revealed in homozygotes in this study. Chiasma frequency in hetero- (1.87) and in homozygous (1.88) males was shown to be higher than in normal ones (1.61). Thus, insertion of recombinationally inert heterochromatic regions leads to increase in the length of genetic map of the chromosome via physical elongation and relaxation of interferential restrictions.

[A new variant of chromosome 1 in the house mouse]. / Novyi variant 1-i khromosomy u domovoi myshi.

In wild mouse populations of Siberia, animals with a new variant of chromosome 1 were found. The total length of this chromosome was 1.3 times as great as the normal homologue. The G-banding technique revealed two additional insertions Is(HSR; 1C5)1Icg and Is(HSR; 1E3)2Icg located between bands 1C5 and 1D, and 1E3 and 1E4, resp. The C-banding of both the insertions was positive and lighter than that of the centromeric heterochromatin. The size of each insertion was approximately 15% of new variant of chromosome 1. No meiotic disturbances were found in heterozygous male mice. Chromosome 1 with insertions has been introduced into the laboratory mouse stock.

[Synapsis in single and double heterozygotes for partially overlapping inversions in chromosome 1 of the house mouse]. / Sinapsis u odinochnykh i dvoinykh geterozigot po chastichno perekryvaiushchimsia inversiiam v pervoi khromosome domovoi myshi.

Electron microscopic analysis of synaptonemal complexes (SC) in single and double heterozygotes for the partially overlapping inversions In(1)1Icg, In(1)1Rk and In(1)12Rk in the Chromosome 1 of the house mouse reveals a dependence of synapsis and synaptic adjustment on the size and location of the inversions and their interaction. In(1)1Icg contains the insertions of inverted repeats Is(HSR: 1C5)1Icg and Is(HSR: 1I)2Icg as well as inverted euchromatic region. The synaptic adjustment of the D loops by shortening of asynapsed parts of the lateral elements of SC belonging to the insertions occurs at late zygotene-early pachytene stage. After that the synaptic adjustment of the inversion loops takes place. A delay in adjustment was found in diheterozygotes In(1)1Icg/In(1)1Rk and In(1)1Icg/In(1)12Rk. Morphological alterations of the asynapted terminal segments of lateral elements preventing synaptic adjustment were found in single and double heterozygotes for In(1)1Rk and In(1)12Rk. Correspondence between the size of asynapted regions and the probability of association of XY and heteromorphic bivalents was revealed.

[Localization of genes on mouse chromosomes by comparing the genetic map and chiasma distribution]. / Opredelenie polozheniia genov na khromosomakh domovoi myshi posredstvom sravneniia geneticheskoi karty i kartiny raspredeleniia khiazm.

It is possible to determine chromosomal position of the genes having definite genetic localization, using chiasmata distribution along the chromosome. This approach was used for subchromosomal mapping of the house mouse genes. It was shown that the chiasmata distributions are different for different chromosomes. The positions of some gene on chromosomes 1, 2, 17 and 19 were determined. The results coincide with those on subchromosomal gene mapping using chromosome translocations and in situ hybridization.

[Effect of heterozygosity for insertions of homogeneously stained regions in chromosome 1 of the house mouse on synapsis in meiotic prophase]. / Vliianie geterozigotnosti po insertsiiam gomogenno okrashivaemykh raionov v 1-i khromosome domovoi myshi na sinapsis v profaze meioza.

Electron microscope analysis of surface-spread synaptonemal complexes (SC) in oocytes and spermatocytes from double cis heterozygotes for Is(HSR; 1C5)1Icg and Is(HSR; 1E3)2Icg was carried out. Aberrant chromosomes were isolated from the feral population of Mus musculus musculus of Novosibirsk. They contain homogeneously stained regions of total length of about 30% of Chr 1 mitotic metaphase. Heteromorphic bivalents of Chr1 with different lengths of the lateral elements of SC and the loop in the intermedial position were revealed in 4.4% spermatocytes and 20% oocytes of heterozygous animals. The loop size depends on the stage of meiosis: it is maximal at late zygotene and decreases up to disappearance during pachytene.

[Effect of double insertion of homogeneously stained regions in chromosome 1 of the house mouse on recombination frequency]. / Vliianie dvoinoi insertsii gomogenno okrashivaemykh raionov v 1-i khromosome domovoi myshi na chastotu rekombinatsii.

By means of genetic and cytogenetic analysis, the effect of cis heterozygosity for two insertions--Is(HSR; 1C5)1Icg and Is (HSR; 1E3)2Icg was studied. It was shown that the proximal point of Is is situated 8 cM distally from the ln gene. Crossing over is completely suppressed in the intermedial part of Chr. 1, where a single chiasma appears in normal mice. The frequency of double chiasmata in heterozygotes is significantly increased. They are localized at precentromeric and pretelomeric parts of Chr. 1. It is supposed that recombination block in the central region leads to a shift of the potential chiasmata in telomeric regions. This shifted telomeric chiasmata, in turn, allow the appearance of the second chiasmata in the centromeric region.

[Meiotic crossing over--not the only source of recombinants in man]. / Meioticheskii krossingover--ne edinstvennyi istochnik rekombinantov u cheloveka.

On the basis of chiasma distributions along bivalents in human male meiosis, genetic lengths were counted for several chromosomal segments. These estimates appeared to be lower than the corresponding genetic lengths produced in the recombination analysis. When al so cytological distances and number of markers used in multilocus mapping were taken into account, the regression estimates of genetic lengths were shown to satisfactorily fit the observed values. This indicates that mitotic crossingover, genetic conversion, mutation and errors in allel's identification in addition to meiotic crossingover, appear to contribute to the observed genetic maps. It is suggested that these namely events, rather than the typing errors suggested by Morton (1991), seem observed over those predicted on the basis of chiasma counts.

[Chromosomal control of chiasma distribution in house mice. Analysis of chiasma distribution in homo- and heterozygotes by inversion in chromosome 1]. / Khromosomnyi kontrol' raspredeleniia khiazm u domovoi myshi. Analiz raspredeleniia khizm u gomo- i geterozigot po inversii v 1-i khromosome.

Examination of chiasma distribution in the chromosome 1 in male mice homo- and heterozygous for distal inversion In(1)12Rk and in normal mice was carried out. No differences in chiasma distribution was found between homozygotes for the inversion and homozygotes for normal chromosome 1. A drastic change in this trait was revealed in heterozygous animals. In heterozygotes, the telomeric segments of SC were asynapsed and unavailable for recombination. This leads to significant decrease in the frequency of bivalents bearing chiasmata in pretelomeric region. In turn, it produced chiasma redistribution in proximal noninverted portion of the bivalent 1. These results could be interpreted as evidence for chromosomal control of chiasma distribution pattern: the distance of certain part of the chromosome from telomere and interference (which also operates at the chromosomal level) are more important for determination of the chiasmata frequency in the given region, than its genetic content.

[An unusual heteromorphic bivalent in the common vole (Microtus arvalis) from Byelarus]. / Neobychnyi geteromorfnyi bivalent u obyknovennykh polevok (Microtus arvalis) iz Belorussii.

Electron microscopic analysis was carried out on the synaptonemal complexes of ten male common voles (Microtus arvalis) caught of 1990 in Byelorussia. In the early pachytene stage of spermatocytes of four males heteromorphic bivalent has been found in one of five large autosomes. In the central region of the bivalent one of the lateral elements is in the form of a D-loop, characteristic of insertion/deletion heterozygotes. However, high-resolution G-band staining of mitotic chromosomes from fibroblasts showed no significant differences in the G-band patterns between homologues.

[The causes of appearance of a double insertion of homogeneously staining regions in the chromosome 1 of house mouse (Mus musculus musculus)]. / Prichiny vozniknoveniia dvoinoi insertsii gomogenno okrashivaemykh raionov v 1-i khromosome domovoi myshi (Mus musculus musculus).

A high resolution analysis of G-band pattern of normal and aberrant chromosome 1 bearing two linked insertions of homogeneously staining regions (HSRs) in the house mouse (Mus musculus musculus) reveals an inverted pattern of the euchromatic region between the HSRs. On the basis of this analysis, a hypothesis on the causes for appearance of the aberrant chromosome was put forward: the double insertion is a result of inversion of the chromosome 1 of Mus musculus domesticus bearing a single long insertion. The proximal breakpoint is localized inside the HSR and the distal one--between subbands E3 and E4. From the point of view of these data, new symbols for the aberrations are proposed: Ls (HSR, 1C5) 1Icg--for the proximal insertion, Is(HSR, 1D)21cg--for the distal one, In (1) 1Icg--for the inverted region, including the bands D, E1-E3 and the insertion Is(HSR 1D)21cg.