How common are common fragile sites in humans: interindividual variation in the distribution of aphidicolin-induced fragile sites.

To obtain an estimate of the variation in common fragile sites (CFSs) among individuals, aphidicolin (APC)-induced chromosomal breakage data were analyzed for 20 karyotypically normal adult humans. As it is specifically designed to meet the analytical requirements for considering fragile sites as presence/absence characters in single individuals, the FSM methodology (Böhm et al., 1995) was used to statistically distinguish fragile from nonfragile sites. These analyses indicated that the APC-induced fragile sites are not ubiquitous but vary extensively among individuals; the per-individual number of fragile sites ranged from as few as seven to as many as 20. Of the 45 different sites identified as fragile, 19 (42%) occurred in more than half of the individuals, but only two sites (3p14 and 16q23) were fragile in all of the individuals; 12 (27% of the total) were fragile in single individuals only. Although these analyses provide statistical confirmation (and initial estimates of population variation) for 43 of the 88 APC-inducible fragile sites currently recognized as occurring among humans, they are consistent with the hypothesis that many of the currently recognized human CFSs have been erroneously identified. These results indicate the need for per-individual statistical identification of CFSs for larger samples of individuals and that studies of particular fragile sites should be conducted on individuals documented to be fragile at the loci under consideration.

Cytogenetics of collared lemmings (Dicrostonyx groenlandicus). II. Meiotic behavior of B chromosomes suggests a Y-chromosome origin of supernumerary chromosomes.

The patterns of synapsis and chiasma formation of the B chromosomes of male collared lemmings (Dicrostonyx groenlandicus) were analyzed by light and electron microscopy and compared to expectations for various hypotheses for the intragenomic origin of supernumerary chromosomes. Pachytene analysis revealed a variety of synaptic configurations including B-chromosome univalents, bivalents and trivalents. In approximately one-half of the pachytene nuclei examined, B chromosomes were in synaptic associations with the normally unpaired portion of the Y chromosome. The B-chromosome configurations at pachynema, including those involving the Y chromosome, were maintained into diakinesis and metaphase I. The meiotic behavior of the B chromosomes was inconsistent with their derivation from centric-fusion products, isochromosome formation, small-autosome polysomy, or the X chromosome. However, the frequent synapsis and apparent recombination between B chromosomes and the Y chromosome implicate this sex chromosome as a possible source of the B chromosomes in collared lemmings.

Systematic implications of chromosomal data from two insular species of Peromyscus from the Gulf of California.

G- and C-banded karyotypes for two insular species of deer mice, Peromyscus slevini and P. sejugis, are described and analyzed relative to the evolutionary relationship of these species to and their inclusion within the P. maniculatus species group. The chromosomal phenotype of P. slevini is unique among all banded karyotypes reported for Peromyscus, and comparison with published karyotypes suggests that P. slevini has systematic affinities with either the P. boylii or P. mexicanus species groups. The karyotypic data for P. sejugis clearly align these mice with P. maniculatus and provide a diagnostic character that supports the specific distinction between these taxa.

Mus and Peromyscus chromosome homology established by FISH with three mouse paint probes.

Fluorescence-labeled DNA probes constructed from three whole house mouse (Mus domesticus) chromosomes were hybridized to metaphase spreads from deer mouse (Peromyscus maniculatus) to identify homologies between the species. Mus Chr 7 probe hybridized strongly to the ad-centromeric two-thirds of Peromyscus Chr 1q. Most of Mus 3 probe hybridized principally to two disjunct segments of Peromyscus Chr 3. Mus Chr 9 probe hybridized entirely to the whole Peromyscus Chr 7. Three Peromyscus linkage groups were assigned to chromosomes, based on linkage homology with Mus. The data also are useful in interpretation of chromosomal evolutionary history in myomorphic rodents.

How common are common fragile sites: variation of aphidicolin-induced chromosomal fragile sites in a population of the deer mouse (Peromyscus maniculatus).

Aphidicolin (APC)-induced chromosomal gaps and breaks were analyzed for ten deer mice (Peromyscus maniculatus) from a natural population. The FSM statistical methodology was used to identify fragile sites as chromosomal loci exhibiting significantly non-random numbers of gaps/breaks in each individual and enabled an assessment of variation in fragile sites among the individuals. The individual deer mice exhibited as few as 7 to as many as 19 of the populational total of 34 sites. Two sites were fragile in all individuals and 13 sites were fragile in single individuals only. Defined by populational frequencies of greater than 50%, high-frequency fragile sites constituted 26% of the populational total. Approximately 35% of the total fragile sites were fragile in 20-40% of the population (low-frequency fragile sites) and about 38% were fragile in single individuals only. Analysis of the data pooled over all individuals identified significantly non-random breakage at 80 sites, 47 of which were not identified as fragile in any single individual. It appears, therefore, that fragile site identifications from pooled data have fostered an inflated estimate of the numbers and frequencies of common fragile sites. Comparison of the fragile site and spontaneous breakage (control) data suggest that APC-induced fragile sites represent regions of chromosomes that experience elevated levels of somatic mutation. Additionally, the occurrence of APC-induced fragile sites at or near the interstitial breakpoints of two pericentric-inversion polymorphisms in this population supports the hypothesis that fragile sites experience an increased rate of meiotic chromosomal mutation and are predisposed to undergo phylogenetic rearrangement.

Cytogenetics of collared lemmings (Dicrostonyx groenlandicus). I. Meiotic behavior and evolution of the neo-XY sex-chromosome system.

Electron-microscopic analysis of surface-spread synaptonemal complexes at pachynema and light-microscopic analysis of chromosomal configurations at diakinesis/metaphase I corroborate the hypothesized neo-XY derivation of the sex chromosomes of Dicrostonyx groenlandicus. Although an intact neo-XY pairing configuration was observed in a relatively small percentage of the pachytene cells in each individual, the high incidence of neo-XY bivalents at diakinesis/metaphase I suggests that the other observed pachytene configurations were artifacts of the physical stresses of the surface-spreading procedure. The very low frequency (0.6%) of univalent neo-X and neo-Y chromosomes at diakinesis and metaphase I is attributable to consistent synapsis and recombination between their homologous autosomally derived segments. The resultant stability of the sex bivalent through metaphase I may have increased the efficacy of sex-chromosome segregation, and thereby played a mechanistic role in the evolutionary incorporation of the neo-XY sex-chromosome constitution in D. groenlandicus.

Minimum sample sizes for identifying chromosomal fragile sites from individuals: Monte Carlo estimation.

A Monte Carlo simulation procedure was used to estimate the exact level of the standardized X2 test statistic (Xs2) for randomness in the FSM methodology for the identification of fragile sites from chromosomal breakage data for single individuals. A random-number generator was used to simulate 10,000 chromosomal breakage data sets, each corresponding to the null hypothesis of no fragile sites for numbers of chromosomal breaks (n) from 1 to 2000 and at three levels of chromosomal band resolution (k). The reliability of the test was assessed by comparisons of the empirical and nominal alpha levels for each of the corresponding values of n and k. These analyses indicate that the sparse and discrete nature of chromosomal breakage data results in large and unpredictable discrepancies between the empirical and nominal alpha levels when fragile site identifications are based on small numbers of breaks (n < 0.5 k). With n > or = 0.5 k, the distribution of Xs2 appears to be stable and non-significant differences in the empirical and nominal alpha levels are generally obtained. These results are inherent to the nature of the data and are, therefore, relevant to any statistical model for the identification of fragile sites from chromosomal breakage data. For FSM identification of fragile sites at alpha = 0.05, we suggest that n > or = 0.5 k is the minimum reliable number of mapped chromosomal breaks per individual.

Susceptibility of heterochromatin to aphidicolin-induced chromosomal breakage.

The distribution of aphidicolin-induced chromosomal lesions was analyzed to determine the relative breakage susceptibility of euchromatin and heterochromatin in the cactus mouse, Peromyscus eremicus. The observed breakage was tested against expected distributions corresponding to the karyotypic proportions of autosomal euchromatin, autosomal heterochromatin, X-chromosomal euchromatin, and X-chromosomal heterochromatin. The distribution of induced breakage was independent of sex but dependent on the individual. In all individuals, there was a highly significant (P < < 0.0001) deficiency in the number of breaks observed as compared to expected in autosomal heterochromatin. Sparse observations in the X chromosome and the absence of breaks in the Y chromosome precluded valid statistical tests of the sex-chromosomal distribution of induced breakage. These data indicate that the autosomal heterochromatin of Peromyscus is resistant to aphidicolin-induced chromosomal breakage and argue against a simple relationship between late replication and a general mechanism for chromosomal fragility.

Identifying chromosomal fragile sites from individuals: a multinomial statistical model.

The inability to identify fragile sites from data for single individuals remains the major obstacle to determining whether these chromosomal loci are predisposed to cancer-causing and evolutionary rearrangements. We describe a novel statistical model that is amenable to data from single individuals and that establishes site-specific chromosomal breakage as nonrandom with respect to the distribution of total breakage. Our method tests incrementally smaller subsets of the data for homogeneity under a multinomial model that assigns equal probabilities to a maximal set of nonfragile sites and unrestricted probabilities to the remaining fragile sites with significantly higher numbers of breaks. We show how standardized Pearson's chi-square (X2) and likelihood-ratio (G2) statistics can be appropriately used to measure goodness-of-fit for sparse contingency (individual-based) data in this model. A sample application of this approach indicates extensive variation in fragile sites among individuals and marked differences in fragile-site inferences from pooled as opposed to per-individual data.

Meiosis in chromosomally heteromorphic goitered gazelle, Gazella subgutturosa (Artiodactyla, Bovidae).

Chromosomal-pairing behaviour was studied in the spermatocytes of individual goitered gazelles which were heteromorphic for a 14/15 Robertsonian translocation and which possessed an autosome-to-X translocation. Both translocations exhibited trivalent pairing configurations in pachytene and diakinesis/metaphase I nuclei. Synapsis of the sex chromosomes during pachynema was followed by end-to-end association of the X and Y during diakinesis/metaphase I. The only univalents identified were of the Y chromosome; Y univalency ranged from 15.9% at pachynema to 5.7% at diakinesis/metaphase I. Robertsonian trivalents exhibited evidence of synaptic adjustment in the paracentromeric region. Chiasmata were formed in most bivalents and trivalents; chiasmata were restricted to the autosomal portion of the autosome-to-XY trivalent. Analysis of metaphase II configurations (secondary spermatocytes) revealed no nondisjunction in individuals homozygous or heterozygous for the Robertsonian translocation. These data are consistent with the hypothesis that neither the autosomal nor the gonosomal heteromorphism reduces the meiotic fitness of male goitered gazelles.

Cytogenetic nomenclature of deer mice, Peromyscus (Rodentia): revision and review of the standardized karyotype. Report of the Committee for the Standardization of Chromosomes of Peromyscus.

A revision of the standardized karyotype of deer mice (Peromyscus) is presented. This revision addresses short-comings of the original standardization, contains a substantial increase in the number of G-band markers and provides a nomenclature for the G-bands of each autosome and the X chromosome. Using the revised standardized karyotype, we specify the particular G-bands or patterns that identify each chromosome and catalog the more problematic chromosome identifications and likely misidentifications. For each chromosome, we present an overview of previously reported variation in euchromatic arrangement and heterochromatic constitution. We then review previous applications of the standardized karyotype and summarize the predominant findings from cytogenetic and cytosystematic studies of Peromyscus and related taxa.

Chromosomal synapsis and the meiotic process in male mesquite lizards, Sceloporus grammicus complex.

Meiosis in males of the F5 cytotype of Sceloporus grammicus was examined through the analysis of synaptonemal complexes (SCs), diakinetic (metaphase I) nuclei, and secondary spermatocytes (metaphase II configurations). These data allowed the establishment of criteria for substaging of zygonema and pachynema, morphological characterization of the SC complement, and comparison of the orientation and segregation of the autosomes and sex chromosomes. The analysis of nuclei from all stages of meiotic prophase I (leptonema through diakinesis) provided a useful means of partitioning the temporal sequence of early meiotic events. Three substages of zygonema (Z1-Z3) were established, based on the extent of synapsis of the microchromosomal and macrochromosomal elements. Synaptic initiation of the autosomes and sex chromosomes was synchronous. Two patterns of macrochromosomal synapsis were observed. Whereas synapsis of the biarmed elements was biterminal (i.e., progressing from both ends of the homologs), synapsis of the acrocentric elements was uniterminal involving only the distal (noncentromeric) ends of the homologs. Unique sex-chromosomal characteristics were not observed in S. grammicus and, therefore, the substaging of pachynema was based on subjective criteria. Examination of diakinesis--metaphase I and metaphase II configurations indicated low levels of diakinetic irregularities with balanced segregation of the autosomal bivalents and the sex-chromosomal trivalent.

Synapsis, recombination, and meiotic segregation in the mesquite lizard, Sceloporus grammicus, complex. I. Pericentric inversion heteromorphism of the F5 cytotype.

Chromosomal pairing and recombination were analyzed in male specimens of Sceloporus grammicus heterozygous for a large pericentric inversion of macrochromosome 4. Analysis of silver-stained synaptonemal complexes (SCs) in surface-spread nuclei revealed that homologously paired inversion loops were not formed. Synapsis of the inverted segments proceeded directly to nonhomologous straight pairing. In some nuclei, this resulted in a configuration that could not be distinguished from homozygous bivalents of similar size. Examination of Giemsa- and silver-stained diakinetic nuclei indicated that crossing-over was limited to the noninverted (homologous) portion of the heteromorphic bivalent. Analysis of secondary spermatocytes (metaphase II configurations) revealed normal disjunction and balanced segregation of the elements of the heteromorphic bivalent. These observations indicate that the inversion heteromorphism does not lead to the production of unbalanced gametes.

Synapsis, recombination, and meiotic segregation in the mesquite lizard, Sceloporus grammicus, complex. II. Fission heteromorphism of the FM2 cytotype and evolution of chromosome 2.

Somatic and meiotic chromosomal and synaptonemal complex techniques were used to characterize the chromosomal complement and to study the fission heteromorphism of chromosome 4 in the FM2 cytotype of Sceloporus grammicus. Analysis of silver-stained somatic metaphases revealed that the nucleolar organizer region in this cytotype is located at the distal end of a pair of medium-sized acrocentric chromosomes, rather than on the largest acrocentric chromosomal pair, as previously reported. This condition is hypothesized to be the result of at least two sequential rearrangements. Analysis of surface-spread zygotene and pachytene nuclei indicated that the components of the chromosome 4 trivalent initiated synapsis at their distal telomeric regions. Although synapsis of the fission trivalent was synchronous with that of the homomorphic autosomal pairs, completion of synapsis was delayed in the trivalent. Associations between the fission trivalent and other autosomal or sex-chromosomal elements occurred in approximately one third of the pachytene nuclei examined. Analysis of secondary spermatocytes (metaphase II configurations) revealed low levels of nondisjunction in fission heterozygotes. These analyses indicate that FM2 individuals heterozygous for the fission rearrangement of chromosome 4 suffer no meiotic deficit.

Heterosynapsis and axial equalization of the sex chromosomes of the northern bobwhite quail.

The pairing behavior of the Z and W chromosomes in the female northern bobwhite quail (Colinus virginianus) was analyzed by electron microscopy of silver-stained synaptonemal complexes (SCs). After autosomal pairing was completed, synapsis of the sex chromosomes initiated at the short-arm end of the W chromosome and one end of the Z chromosome. Synapsis then progressed unidirectionally, producing a sex bivalent in which the entire length of the W axis was paired with an equivalent length of the Z axis. Progressive contraction and asymmetrical twisting of the Z axis ultimately resulted in a fully paired configuration with aligned axial ends. Further contraction of the Z axis reduced the extent of asymmetrical twisting such that only the nonaligned centromeric regions distinguished the SC of the ZW bivalent from SCs of similar-sized autosomes in late-pachytene nuclei. Quantitative analyses indicated that the length of the Z axis shortened significantly during the adjustment process, whereas no significant difference occurred in the length of the W axis. The nonalignment of the centromeric regions during transitional stages of ZW synapsis indicates that direct heterosynapsis of nonhomologous segments, followed by axial equalization of the length inequality, is responsible for the length adjustment during synapsis in the sex chromosomes of the bobwhite quail.

The effect of heterochromatin on synapsis of the sex chromosomes of Peromyscus (Rodentia, Cricetidae).

The pairing behavior of the sex chromosomes in male and female individuals representing seven species of Peromyscus was analyzed by electron microscopy of silver-stained zygotene and pachytene configurations. Six species possess submetacentric or metacentric X chromosomes with heterochromatic short arms. Sex-chromosome pairing in these species is initiated during early pachynema at an interstitial position on the X and Y axes. Homologous synapsis then progresses in a unidirectional fashion towards the telomeres of the X short arm and the corresponding arm of the heterochromatic Y chromosome. The distinctive pattern of synaptic initiation allowed a late-synapsing bivalent in fetal oocytes to be tentatively identified as that of the X chromosomes. In contrast to the other species, Peromyscus megalops possesses an acrocentric X chromosome and a very small Y chromosome. Sex-chromosome pairing in this species is initiated at the proximal telomeric region during late zygonema, and then proceeds interstitially towards the distal end of the Y chromosome. These observations suggest that the presence of X short-arm heterochromatin and corresponding Y heterochromatin interferes with late-zygotene alignment of the pairing initiation sites, thereby delaying XY synaptic initiation until early pachynema. The pairing initiation sites are conserved in the vicinity of the X and Y centromeres in Peromyscus, and consequently the addition of heterochromatin during sex-chromosome evolution essentially displaces these sites to an interstitial position.

Synaptonemal complex analysis of mole rats (Spalax ehrenbergi): unusual polymorphisms of chromosome 1.

Two unusual structural polymorphisms in the largest chromosomal pair of the Israeli mole rat, Spalax ehrenbergi, were analyzed from surface-spread and silver-stained preparations of synaptonemal complexes. A C-band negative polymorphism for the length of the 1p arm was visible as axial length differences during late zygonema and early pachynema. This region underwent synaptic adjustment resulting in a fully paired, mid-pachytene synaptonemal complex with equalized axial lengths. The somatically variable and nonargentophilic secondary constriction in the 1q arm was evident as a distinct silver-stained thickening along the synaptonemal complex. Presence of this structure on the synaptonemal complex varied both among individuals and among cells within individuals. The intraindividual variation of this region is hypothesized to represent differential biochemical activity with its cellular visualization being regulated in a manner similar to that of nucleolus organizer regions.

Unequal crossing over and heterochromatin exchange in the X-Y bivalents of the deer mouse, Peromyscus beatae.

Differences in length of the heterochromatic short arms of the X and Y chromosomes in individuals of Peromyscus beatae are hypothesized to result from unequal crossing over. To test this hypothesis, we examined patterns of synapsis, chiasma formation, and segregation for male P. beatae which were either heterozygous or homozygous for the amount of short-arm sex heterochromatin. Synaptonemal complex analysis demonstrated that mitotic differences in heterochromatic short-arm lengths between the X and Y chromosomes were reflected in early pachynema as corresponding differences in axial element lengths within the pairing region of the sex bivalent. These length differences were subsequently eliminated by synaptic adjustment such that by late pachynema, the synaptonemal complex configurations of the XY bivalent of heterozygotes were not differentiable from those of homozygotes. Crossing over between the heterochromatic short arms of the XY bivalent was documented by the routine appearance of a single chiasma in this region during diakinesis/metaphase I. Sex heterochromatin heterozygotes were characterized by the presence of asymmetrical chiasma between the X and Y short arms at diakinesis/metaphase I and sex chromosomes with unequal chromatid lengths at metaphase II. These data corroborate our hypothesis on the role of unequal crossing over in the production and propagation of X and Y heterochromatin variation and suggest that, in some cases, crossing over can occur during the process of synaptic adjustment.