Nuclear organization in crucifer genomes: nucleolus-associated telomere clustering is not a universal interphase configuration in Brassicaceae

Arabidopsis thaliana has become a major plant research model, where interphase nuclear organization exhibits unique features, including nucleolus-associated telomere clustering. The chromocenter (CC)-loop model, or rosette-like configuration, describes intranuclear chromatin organization in Arabidopsis as megabase-long loops anchored in, and emanating from, peripherally positioned CCs, with those containing telomeres associating with the nucleolus. To investigate whether the CC-loop organization is universal across the mustard family (crucifers), the nuclear distributions of centromeres, telomeres and nucleoli were analyzed by fluorescence in situ hybridization in seven diploid species (2n = 10–16) representing major crucifer clades with an up to 26-fold variation in genome size (160–4260 Mb). Nucleolus-associated telomere clustering was confirmed in Arabidopsis (157 Mb) and was newly identified as the major nuclear phenotype in other species with a small genome (215–381 Mb). In large-genome species (2611–4264 Mb), centromeres and telomeres adopted a Rabl-like configuration or dispersed distribution in the nuclear interior; telomeres only rarely associated with the nucleolus. In Arabis cypria (381 Mb) and Bunias orientalis (2611 Mb), tissue-specific patterns deviating from the major nuclear phenotypes were observed in anther and stem tissues, respectively. The rosette-like configuration, including nucleolus-associated telomere clustering in small-genome species from different infrafamiliar clades, suggests that genomic properties rather than phylogenetic position determine the interphase nuclear organization. Our data suggest that nuclear genome size, average chromosome size and degree of longitudinal chromosome compartmentalization affect interphase chromosome organization in crucifer genomes.     

Reversible chromosome condensation induced in Drosophila embryos by anoxia: visualization of interphase nuclear organization

We have studied the morphology of nuclei in Drosophila embryos during the syncytial blastoderm stages. Nuclei in living embryos were viewed with differential interference-contrast optics; in addition, both isolated nuclei and fixed preparations of whole embryos were examined after staining with a DNA-specific fluorescent dye. We find that: (a) The nuclear volumes increase dramatically during interphase and then decrease during prophase of each nuclear cycle, with the magnitude of the nuclear volume increase being greatest for those cycles with the shortest interphase. (b) Oxygen deprivation of embryos produces a rapid developmental arrest that is reversible upon reaeration. During this arrest, interphase chromosomes condense against the nuclear envelope and the nuclear volumes increase dramatically. In these nuclei, individual chromosomes are clearly visible, and each condensed chromosome can be seen to adhere along its entire length to the inner surface of the swollen nuclear envelope, leaving the lumen of the nucleus devoid of DNA. (c) In each interphase nucleus the chromosomes are oriented in the "telophase configuration," with all centromeres and all telomeres at opposite poles of the nucleus; all nuclei at the embryo periphery (with the exception of the pole cell nuclei) are oriented with their centromeric poles pointing to the embryo exterior.     

Arrangement of chromatin in the nucleus

Summary The factors responsible for producing some degree of order to the arrangement of chromatin in the nucleus are reviewed. They are the following: 1. Chromosomes are attached to the nuclear membrane, nucleolus and intranuclear matrix. As a result they have a relatively fixed position in the nucleus. 2. In some species somatic pairing results in alignment of homologs. This is rare in mammals. 3. The association of ribosomal DNA and 5S DNA with the nucleolous results in the close approximation of the chromosomes carrying these DNA sequences. In man and other animals the most obvious consequence is satellite association. 4. Heterochromatin is condensed onto the inner nuclear membrane and periphery of the nucleolous while genetically active chromatin occupies the more central portion of the nucleus. The results is a peripheral location of late replicating DNA and a central location of early relicating DNA. 5. The DNA replication points tend to be associated with the nuclear matrix. Autoradiography of briefly labelled cells shows a high frequency of grains associated with nuclear matrix material. 6. Heterochromatin association results in chromocenters and ectopic pairing. 7. In addition to all these is the Rabl orientation or alignment of centromeres with centromeres and telomeres with telomeres. This polarization of the chromosomes results from the traction on the centromeres by the spindle fibers. There is no firm evidence for any higher degrees of order that might bring specific functioning genes into close proximity.Supported by NIH Grant GM 15886     

Organisation of complex nuclear domains in somatic mouse cells.

The number and associations of heterochromatin chromocenters, nucleoli, centromeres and telomeres were studied in the nucleus of different somatic cells of Mus domesticus. Fibroblasts of the cell line 3T3, kidney cells (primary culture), and bone marrow cells were used. The above mentioned nuclear and chromosome markers were identified by DAPI/actinomycin D, indirect immunofluorescence with anti-centromere antibodies, silver impregnation for nucleolar proteins and fluorescence in situ hybridisation (FISH) with telomeric probes. The quantitative analysis of the nuclei showed that the pericentromeric heterochromatin is organised in about 18 chromocenters per nucleus in the 3T3 cells, and about seven in kidney and bone marrow cells, having generally a peripheral distribution in the nucleus of all the studied cells. Several aggregated centromeres were participating in each of the chromocenters, about four centromeres per 3T3 cell and about six centromeres per kidney and bone marrow cells. Some of the chromocenters were also in close association with nucleoli. The number of telomeric labels per nucleus was as expected for each chromosome set (2n = 68-70 and 2n = 40). About half of the telomeric signals were loosely aggregated within the heterochromatic blocks while the rest were distributed in the nucleus as unrelated units not bound with chromocenters. The three cell types have complex nuclear territories formed by different chromosomal domains: the pericentromeric heterochromatin, centromeres, proximal telomeres and nucleoli. With the exception of some bone marrow cells, we have not found a nuclear polarisation of the analysed chromosomal markers compatible with the Rabl configuration. However, Rabl anaphasic polarisation allows the contact of centromeric regions making possible that centromeric associations arise. If in addition, associative elements such as constitutive heterochromatin or nucleoli are close to the centromeric regions, like in Mus domesticus chromosomes, then the associations might be consolidated and persist until the interphase. These associations may be the origin of the nuclear domains described here for Mus domesticus somatic cells.     

Yeast Nuclei Display Prominent Centromere Clustering That Is Reduced in Nondividing Cells and in Meiotic Prophase

Chromosome arrangement in spread nuclei of the budding yeast, Saccharomyces cerevisiae was studied by fluorescence in situ hybridization with probes to centromeres and telomeric chromosome regions. We found that during interphase centromeres are tightly clustered in a peripheral region of the nucleus, whereas telomeres tend to occupy the area outside the centromeric domain. In vigorously growing cultures, centromere clustering occurred in ~90% of cells and it appeared to be maintained throughout interphase. It was reduced when cells were kept under stationary conditions for an extended period. In meiosis, centromere clusters disintegrated before the emergence of the earliest precursors of the synaptonemal complex. Evidence for the contribution of centromere clustering to other aspects of suprachromosomal nuclear order, in particular the vegetative association of homologous chromosomes, is provided, and a possible supporting role in meiotic homology searching is discussed.     

Centromere sizes,positions, and movements in the interphase nucleus

Each microspore of the onion Allium fistulosum (n=8) has 8 chromosomes. It is shown that in the microspore the 8 centromeres aggregate to form 2 or 3 centromeric structures. Subsequently, at early mitotic prophase, these aggregates are resolved into 8 separate centromeres and each becomes structurally double. After mitosis the pollen grain contains 2 nuclei, each with 8 separate and distinct centromeres, clustered at the nuclear envelope. As interphase progresses the centromeres of the vegetative nucleus are no longer at the nuclear envelope and they aggregate into 3 or 4 centromeric masses. In the generative nucleus there is less movement. The interphase centromere movements occur in the absence of microtubules. The centromeres range in size from about 0.10 to 0.17 m³ with an average of 0.14 m³ per centromere.     

Effect of Chromosome Tethering on Nuclear Organization in Yeast

Interphase chromosomes in Saccharomyces cerevisiae are tethered to the nuclear envelope at their telomeres and to the spindle pole body (SPB) at their centromeres. Using a polymer model of yeast chromosomes that includes these interactions, we show theoretically that telomere attachment to the nuclear envelope is a major determinant of gene positioning within the nucleus only for genes within 10 kb of the telomeres. We test this prediction by measuring the distance between the SPB and the silent mating locus (HML) on chromosome III in wild–type and mutant yeast strains that contain altered chromosome-tethering interactions. In wild-type yeast cells we find that disruption of the telomere tether does not dramatically change the position of HML with respect to the SPB, in agreement with theoretical predictions. Alternatively, using a mutant strain with a synthetic tether that localizes an HML-proximal site to the nuclear envelope, we find a significant change in the SPB-HML distance, again as predicted by theory. Our study quantifies the importance of tethering at telomeres on the organization of interphase chromosomes in yeast, which has been shown to play a significant role in determining chromosome function such as gene expression and recombination.     

Localization of tandemly repeated DMA sequences in Arabidopsis thaliana

In-situ hybridization to interphase nuclei and chromosomes of Arabidopsis thaliana (2n= 10) shows that there are four sites of rDNA in a diploid nucleus. The sites are located on chromosomes 2 and 4, and the strength of hybridization indicates that copy number is similar at both pairs of sites. Hybridization to trisomic line 4 revealed five hybridization sites. Silver staining of nucleoli demonstrates that all four loci can be active in diploid interphase nuclei. The tandemly repeated probe pAL1 hybridizes near to the centromeres of all five chromosome pairs. In diploid interphase nuclei, 10 sites of hybridization are detected, while 15 are seen in triploid nuclei. The sites of hybridization co-localize with the centromeric heterochromatin visualized by staining DNA with the fluorochrome DAPI. The results demonstrate that molecular cytogenetics can be applied to A. thaliana and high resolution physical chromosome maps can be generated. Both probes may be useful for interphase cytogenetics, where they enable chromosome number and aneuploidy to be examined in tissues without divisions. The physical localization of these hybridization sites provides a starting point for linking RFLP and physical chromosome maps.     

Chromatin arrangements in intact interphase nuclei examined by laser confocal microscopy

Using a laser confocal microscope, chromatin arrangements in intact interphase nuclei were investigated in four plant species. Chromosomes in these plants have specific segments that can be stained with the fluorescent dye chromomycin A₃ (CMA). We stained centromeres inHordeum vulgare, sub-telomeric regions inSecale cereale, satellites inChrysanthemum multicore, and the satellites and the short arms of chromosomes with satellites inHemerocallis middendorfii. The following points were shown: (1) In mitotic interphase nuclei, the centromere and the telomeres of both arms touched the nuclear membrane and had evident polarity. Some CMA-bodies in sub-telomeric regions do not contact the nuclear membrane. (2) Differentiated nuclei had a non-random construction. Polarity of chromosomes is maintained, however, the chromosomes are far apart from the nuclear membrane. (3) Associations in sub-telomeric regions in the interphase nuclei ofSecale cereale were probably due to the association of heterochromatic regions with identical repeated sequences rather than telomere associlations. (4) In interphase nuclei ofChrysanthemum multicore, satellites fused during interphase.     

Cell cycle-dependent specific positioning and clustering of centromeres and telomeres in fission yeast

Fluorescence in situ hybridization (FISH) shows that fission yeast centromeres and telomeres make up specific spatial arrangements in the nucleus. Their positioning and clustering are cell cycle regulated. In G2, centromeres cluster adjacent to the spindle pole body (SPB), while in mitosis, their association with each other and with the SPB is disrupted. Similarly, telomeres cluster at the nuclear periphery in G2 and their associations are disrupted in mitosis. Mitotic centromeres interact with the spindle. They remain undivided until the spindle reaches a critical length, then separate and move towards the poles. This demonstrated, for the first time, that anaphase A occurs in fission yeast. The mode of anaphase A and B is similar to that of higher eukaryotes. In nda3 and cut7 mutants defective in tubulin of a kinesin-related motor, cells are blocked in early stages of mitosis due to the absence of the spindle, and centromeres dissociate but remain close to the SPB, whereas in a metaphase-arrested nuc2 mutant, they reside at the middle of the spindle. FISH is therefore a powerful tool for analyzing mitotic chromosome movement and disjunction using various mutants. Surprisingly, in top2 defective in DNA topoisomerase II, while most chromatid DNAs remain undivided, sister centromeres are separated. Significance of this finding is discussed. In contrast, most chromatid DNAs are separated but telomeric DNAs are not in cut1 mutant. In cut1, the dependence of SPB duplication on the completion of mitosis is abolished. In crm1 mutant cells defective in higher-order chromosome organization, the interphase arrangements of centromeres and telomeres are disrupted.     

串叶松香草Giemsa C带和染色中心研究

以Giemsa C带技术处理串叶松香草根尖细胞染色体(2n=14),全部着丝点及第5和第7对染色体短臂端部显稳定的C带,第6对染色体长臂有两条明显的居间带,其他居间带小而不稳定(重复率不高)。间期细胞核染色体呈Rable构型,其着丝点一极最多出现20个染色中心。统计分析表明,靠近着丝点的短臂端带区和居间带区异染色质有易与着丝点区异染色质融合的倾向。分裂中期Giemsa C带数目与间期染色中心数目存在数量对应关系。     

Effect of Telomeres on the Interphase Location of Adjacent Regions of the Human X Chromosome

Chromosomes occupy specific nonrandom domains in the interphase nucleus of eukaryotic cells. We have used a Chinese hamster-human somatic cell hybrid line containing a single human X chromosome to study the interphase distribution of the Xp telomere using fluorescent in situ hybridization and optical sectioning. A derivative cell line in which the X chromosome has been broken at Xq22-24 and healed by the addition of cloned human telomeric sequences was also studied to determine if introduction of these sequences at a previously interstitial site changed its location in interphase. The endogenous Xp telomere occupies a specific, nonrandom, internal domain. Introduction of a telomere at a previously interstitial site did not alter the interphase nuclear location of that site. The results suggest that nonrandom interphase location of telomeres may not be determined solely by the DNA sequence of the telomere.     

Cytological localization of inverted repeated DNA sequences in Vicia faba

Inverted repeated DNA sequences have been isolated from sheared Vicia faba DNA by hydroxylapatite column chromatography, treated with nuclease S₁, tritiated by the nick translation method and hybridized in situ on squashes of Vicia faba root tips. Silver grains appear grouped in a rather limited portion of interphase nuclei and form a sort of band across them. The central regions of metaphase chromosomes are preferentially labeled, labeling being excluded from telomeres, centromeres and secondary constrictions. These results are briefly discussed in relation to those obtained in other species and the functional significance of inverted repeats.     

Nuclear and territorial topography of chromosome telomeres in human lymphocytes

Nuclear and territorial positioning of p- and q-telomeres and centromeres of chromosomes 3, 8, 9, 13, and 19 were studied by repeated fluorescence in situ hybridization, high-resolution cytometry, and three-dimensional image analysis in human blood lymphocytes before and after stimulation. Telomeres were found on the opposite side of the territories as compared with the centromeres for all chromosome territories investigated. Mutual distances between telomeres of submetacentric chromosomes were very short, usually shorter than centromere-to-telomere distances, which means that the chromosome territory is nonrandomly folded. Telomeres are, on average, much nearer to the center of the cell nucleus than centromeres; q-telomeres were found, on average, more centrally localized as compared with p-telomeres. Consequently, we directly showed that chromosome territories in the cell nucleus are (1) polar and (2) partially oriented in cell nuclei. The distributions of genetic elements relative to chromosome territories (territorial distributions) can be either narrower or broader than their nuclear distributions, which reflects the degree of adhesion of an element to the territory or to the nucleus. We found no tethering of heterologous telomeres of chromosomes 8, 9, and 19. In contrast, both pairs of homologous telomeres of chromosome 19 (but not in other chromosomes) are tethered (associated) very frequently.     

The perichromosomal layer

In addition to genetic information, mitotic chromosomes transmit essential components for nuclear assembly and function in a new cell cycle. A specialized chromosome domain, called the perichromosomal layer, perichromosomal sheath, chromosomal coat, or chromosome surface domain, contains proteins required for a variety of cellular processes, including the synthesis of messenger RNA, assembly of ribosomes, repair of DNA double-strand breaks, telomere maintenance, and apoptosis regulation. The layer also contains many proteins of unknown function and is a major target in autoimmune disease. Perichromosomal proteins are found along the entire length of chromosomes, excluding centromeres, where sister chromatids are paired and spindle microtubules attach. Targeting of proteins to the perichromosomal layer occurs primarily during prophase, and they generally remain associated until telophase. During interphase, perichromosomal proteins localize to nucleoli, the nuclear envelope, nucleoplasm, heterochromatin, centromeres, telomeres, and/or the cytoplasm. It has been suggested that the perichromosomal layer may contribute to chromosome structure, as several of the associated proteins have functions in chromatin remodeling during interphase. We review the identified proteins associated with this chromosome domain and briefly discuss their known functions during interphase and mitosis.     

Meiotic nuclear reorganization: switching the position of centromeres and telomeres in the fission yeast Schizosaccharomyces pombe.

In fission yeast meiotic prophase, telomeres are clustered near the spindle pole body (SPB; a centrosome-equivalent structure in fungi) and take the leading position in chromosome movement, while centromeres are separated from the SPB. This telomere position contrasts with mitotic nuclear organization, in which centromeres remain clustered near the SPB and lead chromosome movement. Thus, nuclear reorganization switching the position of centromeres and telomeres must take place upon entering meiosis. In this report, we analyze the nuclear location of centromeres and telomeres in genetically well-characterized meiotic mutant strains. An intermediate structure for telomere-centromere switching was observed in haploid cells induced to undergo meiosis by synthetic mating pheromone; fluorescence in situ hybridization revealed that in these cells, both telomeres and centromeres were clustered near the SPB. Further analyses in a series of mutants showed that telomere-centromere switching takes place in two steps; first, association of telomeres with the SPB and, second, dissociation of centromeres from the SPB. The first step can take place in the haploid state in response to mating pheromone, but the second step does not take place in haploid cells and probably depends on conjugation-related events. In addition, a linear minichromosome was also co-localized with authentic telomeres instead of centromeres, suggesting that telomere clustering plays a role in organizing chromosomes within a meiotic prophase nucleus.     

The position of interphase chromosomes and late replicating DNA in centromere and telomere regions of Allium cepa L.

Chromosomes in G₁, S, G₂ and early prophase of Allium cepa root tip nuclei are oriented in the same position as telophase chromosomes. The centromeric heteroehromatin is aggregated in a chromocenter at one side of the nucleus, the telomeres scattered at the opposite side. Telomeres appear to associate with other telomeres in interphase in a roughly two by two fashion. Telomere-centromere DNA is late replicating. These results support the conclusion that chromosomes in higher organisms frequently maintain their telophase orientation from the end of telophase, during interphase and well into the next prophase.     

Orientation of interphase chromosomes as detected by Giemsa C-bands

The orientation of Giemsa C-bands has been studied in mitotic and interphase cells of Allium cepa, A. sativum and of Aloe vera. The C-bands in these three species are located at the telomeres, secondary constriction region of the nucleolar chromosomes and the centromeric regions, respectively. Observations in A. cepa and Aloe indicate clearly that the interphase chromosomes are non-random in their orientation and possibly maintain their telophase configuration through the attachment of telomeres and perhaps of kinetochores with the nuclear membrane. Electron micrographs of onion cells also reveal that certain heterochromatic segments are associated with the nuclear membrane. — The nucleolar interstitial C-bands in A. sativum remain free in the nucleoplasm and may come close to each other due to heterochromatic attraction. Such a heterochromatic attraction is also evident between telomeric regions and between centromeres. However, a two by two attachment could not be noticed. A diagrammatic representation of the orientation of interphase chromosomes has been presented.The major part of this work was presented at the First International Congress on Cell Biology, Boston, Sept. 5–10, 1976 (Platform Session 36, J. Cell Biol. 70, 418a (1976)     

Tying SUMO modifications to dynamic behaviors of chromosomes during meiotic prophase of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Summary In budding yeast Saccharomyces cerevisiae, centromeres and telomeres are tethered to the nuclear envelope during premeiotic interphase. Immediately after cells enter meiotic prophase, chromosomes undergo global reorganization, including bouquet formation (telomere clustering), non-homologous centromere coupling, homologous pairing, and assembly/disassembly of synaptonemal complexes. These chromosome dynamics have been implicated in promoting pairing, synapsis, crossover DNA recombination and segregation between homologous chromosomes. This review discusses recent studies related to the role of small ubiquitin-like modifier (SUMO) modification in controlling the overall budding yeast chromosome dynamics during meiotic prophase. This article is dedicated to the 20th anniversary of the Institute of Molecular Biology, Academia Sinica. TFW is grateful to all teachers at IMB, including James C. Wang, Ru-Chih Huang, Ping-Chien Huang, Chung Wang, Henry Y. Sun, Jychian Chen, Ming-Zong Lai, Bon-Chu Chung, and Soo-Chen Cheng. We apologize to those whose work could not be cited due to the brevity of this contribution. TFW was supported by the Investigator Award from Academia Sinica and by the Ta-You Wu Award from the National Science Council, Taiwan.     

Telomere and centromere association tendencies in the human male metaphase complement

Summary Generalized distances between centromeres and between telomeres were statistically analyzed (x ² tests) in 100 trypsin-banded metaphase figures derived from normal males.Analysis of association tendencies on the first column of obtained c-c, p-p, q-p, and p-q histograms showed significant heterochromatin attraction not only between nonacrocentrics and acrocentrics but also between two nonacrocentric chromosome pairs (1 and 16). However since, not all c-heterochromatin-rich chromosomes were involved in associations (pair 5), and conversely, since chromosomes without an important centromeric heterochromatin block were involved in associations (pairs 8 and 11), it is probable that centromeric heterochromatin is not the only factor responsible for chromosome association. Moreover associations occur not only at the centromeres; in our circle analysis of the binding capacity of the telomeres or centromere of one chromosome pair with the telomeres or the centromeres of all other chromosome pairs, we also found preferential associations for T(4,13), T(9,15), T(11,15), T(13,19) T(15,19), T(17,18), T(17,22), and T(19,20).We therefore suggest that heterochromatin is not the only reason for chromosome association and that telomeres may also play an important part in this process.