Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata

In contrast to the situation described for mammals and Drosophila, chromosome territory (CT) arrangement and somatic homologous pairing in interphase nuclei of Arabidopsis thaliana (n = 5) are predominantly random except for a more frequent association of the chromosomes bearing a homologous nucleolus organizer region. To find out whether this chromosome arrangement is also characteristic for other species of the genus Arabidopsis, we investigated Arabidopsis lyrata ssp. lyrata (n = 8), one of the closest relatives of A. thaliana. First, we determined the size of each chromosome and chromosome arm, the sequence type of centromeric repeats and their distribution between individual centromeres and the position of the 5S/45S rDNA arrays in A. lyrata. Then we demonstrated that CT arrangement, homologous pairing and sister chromatid alignment of distinct euchromatic and/or heterochromatic regions within A. lyrata interphase nuclei are similar to that in A. thaliana nuclei. Thus, the arrangement of interphase chromosomes appears to be conserved between both taxa that diverged about 5 million years ago. Since the chromosomes of A. lyrata resemble those of the presumed ancestral karyotype, a similar arrangement of interphase chromosomes is also to be expected for other closely related diploid species of the Brassicaceae family.     

Double in situ hybridization in combination with digital image analysis: a new approach to study interphase chromosome topography

Double in situ hybridization with mercurated and biotinylated chromosome specific DNA probes in combination with digital image analysis provides a new approach to compare the distribution of homologous and nonhomologous chromosome targets within individual interphase nuclei. Here we have used two DNA probes representing tandemly repeated sequences specific for the constitutive heterochromatin of the human chromosomes 1 and 15, respectively, and studied the relative arrangements of these chromosome targets in interphase nuclei of human lymphocytes, amniotic fluid cells, and fibroblasts, cultivated in vitro. We have developed a 2D-image analysis approach which allows the rapid evaluation of large numbers of interphase nuclei. Models to test for a random versus nonrandom distribution of chromosome segments are discussed taking into account the three-dimensional origin of the evaluated 2D-distribution. In all three human diploid cell types the measurements of target-target and target-center distances in the 2D-nuclear image revealed that the labeled segments of the two chromosomes 15 were distributed both significantly closer to each other and closer to the center of the nuclear image than the labeled chromosome 1 segments. This result can be explained by the association of nucleolus organizer regions on the short arm of chromosome 15 with nucleoli located more centrally in these nuclei and does not provide evidence for a homologous association per se. In contrast, evaluation of the interphase positioning of the two chromosome 1 segments fits the random expectation in amniotic fluid and fibroblast cells, while in experiments using lymphocytes a slight excess of larger distances between these homologous targets was occasionally observed. 2D-distances between the labeled chromosome 1 and 15 segments showed a large variability in their relative positioning. In conclusion our data do not support the idea of a strict and permanent association of these homologous and nonhomologous targets in the cell types studied so far.     

Use of two-color fluorescence-tagged transgenes to study interphase chromosomes in living plants

Sixteen distinct sites distributed on all five Arabidopsis (Arabidopsis thaliana) chromosomes have been tagged using different fluorescent proteins and one of two different bacterial operator-repressor systems: (1) a yellow fluorescent protein-Tet repressor fusion protein bound to tet operator sequences, or (2) a green or red fluorescent protein-Lac repressor fusion protein bound to lac operator sequences. Individual homozygous lines and progeny of intercrosses between lines have been used to study various aspects of interphase chromosome organization in root cells of living, untreated seedlings. Features reported here include distances between transgene alleles, distances between transgene inserts on different chromosomes, distances between transgene inserts on the same chromatin fiber, alignment of homologous chromosomes, and chromatin movement. The overall findings are consistent with a random and largely static arrangement of interphase chromosomes in nuclei of root cells. These transgenic lines provide tools for in-depth analyses of interphase chromosome organization, expression, and dynamics in living plants.     

Chromosomal constitution of nucleolus-associated chromatin in man

Summary Use of specific stains permits analysis of the frequency of nucleolus-associated heterochromatin in chromosomes 1 and 9 from human fibroblasts. In 81% of interphase nuclei the heterochromatic segment of both No. 1 chromosomes is associated with the nucleolus, while in 19% only one heterochromatic segment shows such an association with the other occupying a random position in the nucleoplasm. The nucleolar association of chromosome 9 heterochromatin is less constant: in 42.3% of the nuclei both segments are associated with the nucleolus, in 39% of the nuclei only one heterochromatic segment presents such an association, and in 18.7% neither of the two heterochromatic segments is in nucleolar association. In 6% of the cells, one or two chromosome 9 heterochromatic segments are in contact with the nuclear membrane.In situ hybridization using tritium-labeled 28S and 18S RNA shows that in the interphase nucleus the acrocentric short arms, carriers of ribosomal cistrons, are associated with the nucleolus.These observations demonstrate the complexity of the nucleolus-associated chromatin which, in addition to segments of chromosomes 1, 9, 13, 14, 15, 21 and 22, may include the Y chromosome. They also confirm that the nucleolus constitutes one of the orientation points determining the relative localization of chromosomes in the interphase nucleus.     

Satellited Y chromosomes: Structure,origin, and clinical significance

Summary Three cases of inherited satellited Y chromosomes (Yqs) were analysed using several cytogenetic techniques. The cytogenetic data of the 14 cases of Yqs chromosomes described to date were reviewed. All Yqs chromosomes carry an active nucleolus organizer region (NOR) in their long arm and must have developed from translocations involving the short arms of the acrocentric autosomes. The structure of the heterochromatic satellite region in the Yqs chromosomes shows conspicuous inter-familial differences; this permits the reconstruction of the translocations from which the various Yqs were derived. Some causal factors leading to the development of Yqs chromosomes are considered: the specific localization of the four satellite DNAs and highly methylated DNA sequences in the karyotype, and some new experimental data on the spatial arrangement of heterochromatic regions in interphase nuclei. These provide distinct evidence for a preferential involvement of the autosomes 15 and 22 in the translocations with the Y heterochromatin. All clinical reports documenting Yqs males born with malformations were reviewed. It appears that the presence of an extra NOR and NOR-associated heterochromatin in the Yqs chromosomes does not cause any phenotypic abnormalities (as long as the Y euchromatin is intact). The possibility that a Yqs chromosome predisposes to non-disjunction and/or to translocations of other chromosomes is discussed.     

Ag-NOR staining in the Bennett wallaby, Macropus rufogriseus: evidence for dosage compensation

Silver staining of cells in metaphase and interphase nuclei of both sexes of the Bennett wallaby, Macropus rufogriseus, has shown that (1) the nucleolus organizer region (NOR) is located only on the X chromosome (single Ag-NOR); (2) both X chromosomes in the female cells stain with silver; (3) the amounts of silver staining of metaphase chromosomes and interphase nuclei of both sexes are very similar; (4) the single X chromosome is hyperactive in male cells to equalize the expression of rRNA genes in the female cells with two X chromosomes; and (5) the mechanism of dosage compensation for rRNA genes in this species is similar to that reported for Drosophila salivary gland cells.     

The positioning of rye homologous chromosomes added to wheat through the cell cycle in somatic cells untreated and treated with colchicine

The arrangement of chromosome pairs 5RL and 7R added to the wild type and the ph1b mutant line of hexaploid wheat are analyzed in 2N somatic root tip cells during the cell cycle relative to the arrangement that chromosomes 5RL show in 4N tapetal cells produced after colchicine treatment. Both homologous chromosome pairs are identified at interphase and mitosis by fluorescence in situ hybridization. In nuclei at interphase, chromosomes appear as discrete domains that show the Rabl orientation. Homologous chromosomes are predominantly non-associated and their positioning seems not to be influenced by the Ph1 gene that suppresses homoeologous meiotic pairing. This pattern of arrangement contrasts with the high level of somatic pairing that sister chromosomes show in the interphase that follows chromosome duplication induced by colchicine. Disruption of pairing observed in some 4N nuclei is produced at c-anaphase which suggests no topological redistribution of homologues during conformation of the new nucleus. Homologous chromosomes show no predominant arrangement in ellipsoidal metaphase plates, which contrasts with the preferential opposite location of homologues in human prometaphase rosettes. Differences between chromosomes in the variation of the length through the cell cycle and in the chromatin morphology when the Ph1 is absent suggest different patterns of chromatin condensation in both chromosomes.     

Analysis of substage associations in prophase I of meiosis in floral buds of wild-type Arabidopsis thaliana (Brassicaceae)

We developed an improved cytological protocol for producing high quality, light microscope images of plant meiotic chromosomes. Because the technique works on species with small genomes and thick microsporocyte cell walls, it should be useful for studying the wild relatives of Arabidopsis and other eudicots with small genomes. Combining this improved fixation protocol with our new analysis of associated substages in floral buds, we can unambiguously assign individual meiotic cells to particular substages of prophase I in Arabidopsis thaliana, even for difficult distinctions such as that between late zygotene or early diplotene. In this report we provide the first estimate of the individual duration of the zygotene and pachytene substages (4.8 h and 10.0 h, respectively) in A. thaliana. We also have examined the diffuse substage of prophase I and report that during this post-pachytene substage, nuclei retain the association of homologous nucleolus organizer regions and homologous centromeres, despite the generally diffuse chromatin and generally unpaired chromosome regions. Additionally, we have observed that centromeric regions of the chromosomes of diffuse-stage nuclei are highly condensed, more so than those of any other substage of prophase I.     

HETEROCHROMATIN IN HUMAN MALE LEUKOCYTES

Tritiated thymidine was added to peripheral blood cultures containing phytohemagglutinin so that DNA synthesis in interphase nuclei of white blood cells in the human male could be studied. After 57 hours in culture, a large heterochromatic body with a central position is seen in unlabeled Feulgen-stained nuclei. In labeled nuclei in which DNA synthesis was taking place in both the eu- and heterochromatin at the time the thymidine became available, the heterochromatin shows a higher number of silver grains per unit area, accompanied by a stronger Feulgen reaction, an indication of its higher DNA content. The time of DNA synthesis in the heterochromatin blocks is different from that in the surrounding euchromatin. The large heterochromatic block is composed of chromosome segments gathered together around the nucleolus but it is not part of this organelle. In preparations stained with azure A and acid fuchsin for demonstrating both the nucleolus and the chromosomes, six distinctly heteropyenotic chromosome segments can be seen associated with the nucleolus. Cells of all size categories were found to incorporate tritiated thymidine. The distinct appearance of autosomal heterochromatin in white blood cells may be the result of the new physiological conditions to which the cells are subjected in the medium containing phytohemagglutinin.     

Chromosome territory arrangement and homologous pairing in nuclei of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> are predominantly random except for NOR-bearing chromosomes

Differential painting of all five chromosome pairs of Arabidopsis thaliana revealed for the first time the interphase chromosome arrangement in a euploid plant. Side-by-side arrangement of heterologous chromosome territories and homologous association of chromosomes 1, 3 and 5 (on average in 35–50% of nuclei) are in accordance with the random frequency predicted by computer simulations. Only the nucleolus organizing region (NOR)-bearing chromosome 2 and 4 homologs associate more often than randomly, since NORs mostly attach to a single nucleolus. Somatic pairing of homologous 100 kb segments occurs less frequently than homolog association, not significantly more often than expected at random and not simultaneously along the homologs. Thus, chromosome arrangement in Arabidopsis differs from that in Drosophila (characterized by somatic pairing of homologs), in spite of similar genome size, sequence organization and chromosome number. Nevertheless, in up to 31.5% of investigated Arabidopsis nuclei allelic sequences may share positions close enough for homologous recombination.Electronic Supplementary Material Supplementary material is available for this article at .     

Chromosome banding in Amphibia

The distribution and quantity of constitutive heterochromatin and of the nucleolus organizer regions (NORs) on the chromosomes of 22 species of bufonids and hylids (Amphibia, Anura) was investigated. Three different kinds of constitutive heterochromatin were found and the frequency of brightly fluorescing heterochromatic regions was remarkably high. On almost all chromosomes there is centric and telomeric heterochromatin. Quantitative estimates of heterochromatin demonstrate that large DNA differences among closely related species can not be attributed to differing quantities of constitutive heterochromatin. In all species investigated, only one homologous pair of NORs was found, which lies preferentially in the proximal and interstitial segments of the long chromosome arms. The NORs are always associated with constitutive heterochromatin on both sides. The size variability between homologous NORs is very high. In the euchromatic regions of the metaphase chromosomes, neither Q- nor G-bands can be demonstrated; this can be attributed to an extremely strong contraction of the anuran chromosomes. On the basis of these results various mechanism of the chromosomal evolution in Anura are discussed.     

Arrangement of prematurely condensed chromosomes in cultured cells and lymphocytes of the Indian muntjac

Premature chromosome condensation (PCC) was induced in order to study the arrangement of muntjac chromosomes in the interphase nuclei of proliferating and resting cells with respect to their polarity and the spatial relationship between them. The data were compared with the situation in in situ fixed and colcemid blocked metaphases. It appears that in rapidly dividing cells almost all G₁- and G₂ interphase chromosomes exhibit the Rabl type polarized orientation. This pattern still predominates in G₀ lymphocytes which may have been arrested at this stage for some months or even years. — The location of the small chromosome Y₂ was found to be central in normal metaphases but peripheral in colcemid blocked mitoses. The behavior in the premature condensed chromosome preparations was intermediate. Measurements of centromere distances between all possible pairs of chromosomes as well as on the relative position of chromosomes in circular spreads revealed no evidence for homologous somatic association during interphase and metaphase or any other suprachromosomal ordering principle. Interphase chromosome orientation seems to be solely the result of chromosome arrangement of the foregoing anaphase. Association between heterochromatic regions or the nucleolus organizers did not substantially influence this pattern. There is no support for speculations that in mammalian cells close proximity of homologoues sites is instrumental in functional cooperation.     

Interphase chromosome order: A proposal

A model for the arrangement of chromosomes in interphase nuclei is proposed. The model assumes that interphase chromosomes have a Rabl orientation (a relic telophase arrangement). During interphase and prophase telomeres are attached to the nuclear envelope often in pairs. The association of telomeres, homologous or nonhomologous, is based on similarity of arm lengths and occurs at the time the nuclear envelope reforms. At this stage arm lengths will vary to some extent due to the amount of uncoiling etc. The sequence of chromosomes resulting from telomere-telomere pairing may vary among cells, but the number of arrangements will be restricted by arm length similarities.The ramifications of this model on melotic pairing, the constant attachment of chromosomes to some structure throughout the cell cycle, the distribution of genes within nuclei, and chromosome evolution are raised.     

Chromosome organization and dynamics in plants

The past few years have brought renewed interest in understanding the dynamics of chromosomes in interphase cells as well as during cell division, particularly meiosis. This research has been fueled by new imaging methods, particularly three-dimensional, high-resolution, and live microscopy. Major contributors are also new genetic tools that allow elucidation of mechanisms controlling chromosome behavior. Recent studies in plants have explored chromatin arrangement in interphase nuclei, chromosome interactions and movement during meiotic prophase I, and mechanisms that ensure correct segregation of chromosomes during anaphase. These studies shed light on chromosome dynamics in a small-genome plant Arabidopsis thaliana, as well as in plants with large and complex genomes of polyploid origin, such as wheat and maize.     

Arrangement of centromeres in mouse cells

Applying a staining procedure which reveals constitutive heterochromatin to cytological preparations of the mouse (Mus musculus), one detects heterochromatin pieces at the centromeric areas of all chromosomes except the Y. The Y chromosome is somewhat heteropyenotic in general but possesses no intensely stained centromeric heterochromatin. The arrangement of the centromeric heterochromatin in interphase cells is apparently specific for a given cell type. In meiotic prophase, centromeric heterochromatin may form clusters among bivalents. From the location of the centromeric heterochromatin of the X chromosome in the sex bivalent, it is concluded that the association between the X and Y (common end) in meiosis is limited to the distal portions of the sex elements.