The role of the chromocenter in nonrandom meiotic segregation of nonhomologous chromosomes in Drosophila melanogaster females

The evidence supporting universal significance of physical links between pericentromeric regions of homologous chromosomes for their bipolar orientation during the first meiotic division is discussed. The pericentromeric chiasmata between homologs or (in the absence of the latter) chromocentric links between nonhomologs, which are preserved until prometaphase, compensate for the disturbed binding between homologous pericentromeric regions in both structural or locus mutants. When the links between nonhomologs are involved, interchromosomal effects on chromosome disjunction and nonhomologous pairing were revealed by the genetic methods. An explanation suggested for genetic events observed during Drosophila meiosis conforms with the original, cytogenetically proved model of the orderly two-ring chromocenter formation and reorganization.     

Chromocentral nature of interchromosome connections coorienting nonhomologous chromosomes in meiosis of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> females

Data are presented in favor of universal significance of physical connections between pericentromeric regions of homologs in their orientation to the opposite poles of the first meiotic division in Drosophila melanogaster. Disturbances in the formation of such connections caused by structural or locus mutations are compensated for by the presence of pericentromeric chiasmata between homologs or (in the case of their absence) by chromocentral connections between nonhomologs being preserved up to the prometaphase. In the latter case, an interchromosome effect on chromosome disjunction and nonhomologous pairing is registered by genetic methods. Inhibition of the formation of the division spindle fibers during prometaphase of meiosis 1 by the long-term action of colcemide promotes the retention of connections between paired nonexchanged homologs and between nonhomologous chromosomes with abnormal homologous pairing because of heterozygosity for numerous inversions and transpositions (X and autosome 2). These connections are registered cytologically. Cytologically registered are also connections between normal X chromosomes and metacentric compounds by the arms of autosome 2 (C(2L)RM, C(2R)RM), which is the known case of the interchromosome effect on chromosome nondisjunction. It is supposed that cytologically detected associations between compounds are realized through a normal mechanism, as a result of interaction and formation of orienting connections between the homologous pericentromeric regions of these compounds. Cytological evidence is presented for colocation of compounds in the chromocentrally organized nucleus of somatic and germline cells.     

Pericentromeric chromatin reorganisation follows the initiation of recombination and coincides with early events of synapsis in cereals

The reciprocal exchange of genetic information between homologous chromosomes during meiotic recombination is essential to secure balanced chromosome segregation and to promote genetic diversity. The chromosomal position and frequency of reciprocal genetic exchange shapes the efficiency of breeding programmes and influences crop improvement under a changing climate. In large genome cereals, such as wheat and barley, crossovers are consistently restricted to subtelomeric chromosomal regions, thus preventing favourable allele combinations being formed within a considerable proportion of the genome, including interstitial and pericentromeric chromatin. Understanding the key elements driving crossover designation is therefore essential to broaden the regions available for crossovers. Here, we followed early meiotic chromatin dynamism in cereals through the visualisation of a homologous barley chromosome arm pair stably transferred into the wheat genetic background. By capturing the dynamics of a single chromosome arm at the same time as detecting the undergoing events of meiotic recombination and synapsis, we showed that subtelomeric chromatin of homologues synchronously transitions to an open chromatin structure during recombination initiation. By contrast, pericentromeric and interstitial regions preserved their closed chromatin organisation and become unpackaged only later, concomitant with initiation of recombinatorial repair and the initial assembly of the synaptonemal complex. Our results raise the possibility that the closed pericentromeric chromatin structure in cereals may influence the fate decision during recombination initiation, as well as the spatial development of synapsis, and may also explain the suppression of crossover events in the proximity of the centromeres.     

Synaptonemal complex spreading in Allium cepa and A. fistulosum

The general features and fine structure of homologous chromosome alignment and pairing have been investigated in two species of Allium (A. fistulosum and A. cepa), which have similar karyotypes but very different patterns of chiasma distribution. Although there is no support for the occurrence of a general pre-meiotic alignment of homologous chromosomes, both species show some alignment of homologues as an immediate prelude to synaptonemal complex (SC) formation. In both species pairing usually commences at sub-terminal sites and is succeeded by numerous separate intercalary initiations of pairing in interstitial and distal regions and then in proximal regions. The last parts to pair, in both species, are pericentromeric and telomeric regions. There is, therefore, no evident relationship between the sequence of pairing and chiasma distribution in these species. Regularly alternating convergences and divergences of aligned axial cores (ACs), termed multiple association sites, are frequently observed. It is proposed that these represent potential pairing initiation sites and from observations on their spatial distribution it is argued that they may be evenly distributed through most of the genome. Small spherical or ellipsoid nodules are found at association sites and between closely aligned ACs which persist in the SC segments present during zygotene, but most of them disappear abruptly at the end of zygotene. These are termed zygotene nodules (ZN) and it is proposed that they are involved in matching corresponding sites on homologous chromosomes as well as possibly having a recombinational role. Their composition, structure, mode of action and relationship to pachytene recombination nodules are at present unknown.     

Unusual case of 18p- syndrome: diagnosis using a cloned DNA fragment

The patient with atypical clinic picture of 18p- syndrome is described. The in situ hybridization technique was used to localize chromosome 18-specific cloned sequence to metaphase chromosomes of the proband. The predominant hybridization was found in pericentromeric regions of homologous chromosome 18. The amount of pericentromeric DNA measured by in situ hybridization was different in homologous chromosomes and the number of radioactive grains was statistically greater in the normal chromosome 18 than in the chromosome 18p-. The cause of asymmetrical hybridization of probes to homologous chromosomes 18 is discussed. The results obtained indicate that this probe may be useful in clinical cytogenetics for identification of chromosome 19 in metaphase and interphase cells, determination of breakpoints or studies of pericentromeric DNA polymorphisms.     

A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function

Aegilops tauschii (Coss.) Schmal. (2n=2x=14, DD) (syn. A. squarrosa L.; Triticum tauschii) is well known as the D-genome donor of bread wheat (T. aestivum, 2n=6x=42, AABBDD). Because of conserved synteny, a high-density map of the A. tauschii genome will be useful for breeding and genetics within the tribe Triticeae which besides bread wheat also includes barley and rye. We have placed 249 new loci onto a high-density integrated cytological and genetic map of A. tauschii for a total of 732 loci making it one of the most extensive maps produced to date for the Triticeae species. Of the mapped loci, 160 are defense-related genes. The retrotransposon marker system recently developed for cultivated barley (Hordeum vulgare L.) was successfully applied to A. tauschii with the placement of 80 retrotransposon loci onto the map. A total of 50 microsatellite and ISSR loci were also added. Most of the retrotransposon loci, resistance (R), and defense-response (DR) genes are organized into clusters: retrotransposon clusters in the pericentromeric regions, R and DR gene clusters in distal/telomeric regions. Markers are non-randomly distributed with low density in the pericentromeric regions and marker clusters in the distal regions. A significant correlation between the physical density of markers (number of markers mapped to the chromosome segment/physical length of the same segment in m) and recombination rate (genetic length of a chromosome segment/physical length of the same segment in m) was demonstrated. Discrete regions of negative or positive interference (an excess or deficiency of crossovers in adjacent intervals relative to the expected rates on the assumption of no interference) was observed in most of the chromosomes. Surprisingly, pericentromeric regions showed negative interference. Islands with negative, positive and/or no interference were present in interstitial and distal regions. Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed.     

Human (Homo sapiens) and chimpanzee (Pan troglodytes) share similar ancestral centromeric alpha satellite DNA sequences but other fractions of heterochromatin differ considerably

The euchromatic regions of chimpanzee (Pan troglodytes) genome share approximately 98% sequence similarity with the human (Homo sapiens), while the heterochromatic regions display considerable divergence. Positive heterochromatic regions revealed by the CBG-technique are confined to pericentromeric areas in humans, while in chimpanzees, these regions are pericentromeric, telomeric, and intercalary. When human chromosomes are digested with restriction endonuclease AluI and stained by Giemsa (AluI/Giemsa), positive heterochromatin is detected only in the pericentromeric regions, while in chimpanzee, telomeric, pericentromeric, and in some chromosomes both telomeric and centromeric, regions are positive. The DA/DAPI technique further revealed extensive cytochemical heterogeneity of heterochromatin in both species. Nevertheless, the fluorescence in situ hybridization technique (FISH) using a centromeric alpha satellite cocktail probe revealed that both primates share similar pericentromeric alpha satellite DNA sequences. Furthermore, cross-hybridization experiments using chromosomes of gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) suggest that the alphoid repeats of human and great apes are highly conserved, implying that these repeat families were present in their common ancestor. Nevertheless, the orangutan's chromosome 9 did not cross-hybridize with human probe. The euchromatic regions of chimpanzee (Pan troglodytes) genome share approximately 98% sequence similarity with the human (Homo sapiens), while the heterochromatic regions display considerable divergence. Positive heterochromatic regions revealed by the CBG-technique are confined to pericentromeric areas in humans, while in chimpanzees, these regions are pericentromeric, telomeric, and intercalary. When human chromosomes are digested with restriction endonuclease AluI and stained by Giemsa (AluI/Giemsa), positive heterochromatin is detected only in the pericentromeric regions, while in chimpanzee, telomeric, pericentromeric, and in some chromosomes both telomeric and centromeric, regions are positive. The DA/DAPI technique further revealed extensive cytochemical heterogeneity of heterochromatin in both species. Nevertheless, the fluorescence in situ hybridization technique (FISH) using a centromeric alpha satellite cocktail probe revealed that both primates share similar pericentromeric alpha satellite DNA sequences. Furthermore, cross-hybridization experiments using chromosomes of gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) suggest that the alphoid repeats of human and great apes are highly conserved, implying that these repeat families were present in their common ancestor. Nevertheless, the orangutan's chromosome 9 did not cross-hybridize with human probe. © 1995 Wiley-Liss, Inc.     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

18p− Syndrome: an unusual case and diagnosis by in situ hybridization with chromosome 18-specific alphoid DNA sequence

Summary A patient with an atypical clinical picture of 18p^– syndrome is described. By the in situ hybridization technique we localized the chromosome 18-specific cloned repetitive sequence to metaphase chromosomes of the patient. The predominant hybridization of the probe was found in pericentromeric regions of homologous chromosomes 18. The amount of pericentromeric DNA measured by in situ hybridization differed between homologous chromosomes; and the number of radioactive grains was statistically greater in the normal chromosome 18 than in the aberrant chromosome 18p^–. The results indicate that this probe may be useful in clinical cytogenetics for identification of aberrant chromosomes, localization of breakpoints, and studies of C-band DNA polymorphism of chromosome 18.     

Polytene chromosome maps in four species of tsetse flies Glossina austeni, G. pallidipes, G. morsitans morsitans and G. m. submorsitans (Diptera: Glossinidae): a comparative analysis

Photographic polytene chromosome maps from pupal trichogen cells of four tsetse species, Glossina austeni, G. pallidipes, G. morsitans morsitans and G. m. submorsitans were constructed and compared. The homology of chromosomal elements between the species was achieved by comparing banding patterns. The telomeric and subtelomeric chromosome regions were found to be identical in all species. The pericentromeric regions were found to be similar in the X chromosome and the left arm of L1 chromosome (L1L) but different in L2 chromosome and the right arm of L1 chromosome (L1R). The L2 chromosome differs by a pericentric inversion that is fixed in the three species, G. pallidipes, G. morsitans morsitans and G. m. submorsitans. Moreover, the two morsitans subspecies appeared to be homosequential and differ only by two paracentric inversions on XL and L2L arm. Although a degree of similarity was observed across the homologous chromosomes in the four species, the relative position of specific chromosome regions was different due to chromosome inversions established during their phylogeny. However, there are regions that show no apparent homology between the species, an observation that may be attributed to the considerable intra—chromosomal rearrangements that have occurred following the species divergence. The results of this comparative analysis support the current phylogenetic relationships of the genus Glossina.     

Puzzling Chromosome Behavior in Triploid Females of Drosophila melanogaster

Based on a particular formation of the chromocenter and trivalents in triploid Drosophila females, as well as on asynapsis in pericentromeric regions (which is a result of trivalent competition), an explanation for the increased frequency of crossing over and nonrandom segregation of the X chromosomes and autosomes in the first meiotic division is suggested. It is proposed that a delay in pairing of the pericentromeric heterochromatic chromosome regions combined into a single chromocenter leads to the following: (1) formation of the heteroduplex structures (X structures) takes more time and, consequently, their number and the frequency of crossing over in the paired chromosome regions increases; (2) in nonhomologous chromosomes, the chromocentral connections, which normally degrade in prometaphase, are retained to fulfill a function of coorientation during the first meiotic division.     

Cloned fragment of human alphoid DNA--a molecular marker of the pericentromeric region of chromosome 18

From the library of cloned fragments of human DNA we have isolated two recombinant plasmids containing alphoid DNA sequences pBRHS13, pBRHS65. Both cloned sequences hybridized in situ predominantly to pericentromeric regions of chromosome 18 and with less intensity to pericentromeric regions of chromosomes 2, 9, 20, and were characterized by populational copy number polymorphism in homologous chromosomes. These sequences may appear very useful in the diagnostics and cytogenetic analysis of chromosomal aberrations and in studies of polymorphisms of heterochromatic regions of human chromosomes.     

Characterization of the human lineage-specific pericentric inversion that distinguishes human chromosome 1 from the homologous chromosomes of the great apes

The human and chimpanzee genomes are distinguishable in terms of ten gross karyotypic differences including nine pericentric inversions and a chromosomal fusion. Seven of these large pericentric inversions are chimpanzee-specific whereas two of them, involving human chromosomes 1 and 18, were fixed in the human lineage after the divergence of humans and chimpanzees. We have performed detailed molecular and computational characterization of the breakpoint regions of the human-specific inversion of chromosome 1. FISH analysis and sequence comparisons together revealed that the pericentromeric region of HSA 1 contains numerous segmental duplications that display a high degree of sequence similarity between both chromosomal arms. Detailed analysis of these regions has allowed us to refine the p-arm breakpoint region to a 154.2 kb interval at 1p11.2 and the q-arm breakpoint region to a 562.6 kb interval at 1q21.1. Both breakpoint regions contain human-specific segmental duplications arranged in inverted orientation. We therefore propose that the pericentric inversion of HSA 1 was mediated by intra-chromosomal non-homologous recombination between these highly homologous segmental duplications that had themselves arisen only recently in the human lineage by duplicative transposition.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .Justyna M. Szamalek and Violaine Goidts are contributed equally to the paper.     

Recognition sites and coordinate control of recombination in Schizophyllum

The genetic control of recombination in two chromosomal regions was studied in dikaryons of Schizophyllum commune with joint control of recombination in the A and B factors. The role of the controlled regions in the determination of their recombination frequencies was studied by substituting one or the other or both by homologous segments. The B factor was shown to affect both its own and the A factors' recombination frequency. A model of genetic control of recombination in several regions is proposed. The model is based on identical recognition sites within the jointly controlled segments. It is consistent with the fact that jointly-controlled segments can show either negative or positive correlation between their recombination frequencies.     

Identification,characterisation and clinical applications of cosmids from the telomeric and centromeric regions of the long arm of chromosome 22

Using human telomeric repeats and centromeric alpha repeats, we have identified adjacent single copy cosmid clones from human chromosome 22 cosmid libraries. These single copy cosmids were mapped to chromosome 22 by fluorescence in situ hybridisation (FISH). Based on these cosmids, we established contigs that included part of the telomeric and subtelomeric regions, and part of the centromeric and pericentromeric regions of the long arm of human chromosome 22. Each of the two cosmid contigs consisted of five consecutive steps and spanned approximately 100–150 kb at both extreme ends of 22q. Moreover, highly informative polymorphic markers were identified in the telomeric region. Our results suggest that the telomere specific repeat (TTAGGG) _n encompasses a region that is larger than 40 kb. The cosmid contigs and restriction fragment length polymorphism markers described here are useful tools for physical and genetic mapping of chromosome 22, and constitute the basis of further studies of the structure of the subtelomeric and pericentromeric regions of 22q. We also demonstrate the use of these clones in clinical diagnosis of different chromosome 22 aberrations by FISH.     

Genetic linkage and heterogeneity in type I Charcot-Marie-Tooth disease (hereditary motor and sensory neuropathy type I).

The segregation patterns of DNA markers from the pericentromeric regions of chromosomes 1 and 17 were studied in seven pedigrees segregating an autosomal dominant gene for Charcot-Marie-Tooth neuropathy type I (CMT I; hereditary motor and sensory neuropathy I). A multilocus analysis with four markers (pMCR-3, pMUC10, FY, and pMLAJ1) spanning the pericentromeric region of chromosome 1 excluded the CMT I gene from this region in six pedigrees but gave some evidence for linkage to the region of Duffy in one pedigree. Linkage of the CMT I gene to markers in the pericentromeric region of chromosome 17 (markers pA10-41, pEW301, p3.6, and pTH17.19) was established; however, in these seven pedigrees homogeneity analysis with chromosome 17 markers detected significant genetic heterogeneity. This analysis suggested that three of the seven pedigrees are not linked to this same region. Overall, two of the seven CMT I pedigrees were not linked to markers tested from chromosomes 1 or 17. These results confirm genetic heterogeneity in CMT I and implicate the existence of a third autosomal locus, in addition to a locus on chromosome 17, and a probable locus on chromosome 1. This evidence of etiological heterogeneity, supported by statistical tests, will have to be taken into consideration when fine-structure genetic maps of the regions around CMT I are constructed.     

Young but not relatively old retrotransposons are preferentially located in gene‐rich euchromatic regions in tomato (Solanum lycopersicum) plants

Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination‐suppressed heterochromatin regions, and that young elements are preferentially located in the gene‐rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non‐random distribution of LTR retrotransposons in tomato plants.     

A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function

Aegilops tauschii (Coss.) Schmal. (2n = 2x = 14, DD) (syn. A. squarrosa L.; Triticum tauschii) is well known as the D-genome donor of bread wheat (T. aestivum, 2n = 6x = 42, AABBDD). Because of conserved synteny, a high-density map of the A. tauschii genome will be useful for breeding and genetics within the tribe Triticeae which besides bread wheat also includes barley and rye. We have placed 249 new loci onto a high-density integrated cytological and genetic map of A. tauschii for a total of 732 loci making it one of the most extensive maps produced to date for the Triticeae species. Of the mapped loci, 160 are defense-related genes. The retrotransposon marker system recently developed for cultivated barley (Hordeum vulgare L.) was successfully applied to A. tauschii with the placement of 80 retrotransposon loci onto the map. A total of 50 microsatellite and ISSR loci were also added. Most of the retrotransposon loci, resistance (R), and defense-response (DR) genes are organized into clusters: retrotransposon clusters in the pericentromeric regions, R and DR gene clusters in distal/telomeric regions. Markers are non-randomly distributed with low density in the pericentromeric regions and marker clusters in the distal regions. A significant correlation between the physical density of markers (number of markers mapped to the chromosome segment/physical length of the same segment in microm) and recombination rate (genetic length of a chromosome segment/physical length of the same segment in microm) was demonstrated. Discrete regions of negative or positive interference (an excess or deficiency of crossovers in adjacent intervals relative to the expected rates on the assumption of no interference) was observed in most of the chromosomes. Surprisingly, pericentromeric regions showed negative interference. Islands with negative, positive and/or no interference were present in interstitial and distal regions. Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed.