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.     

Molecular organization of DNA in chromosomes

Metaphase chromosomes of Chinese hamster and lampbrush chromosomes of Triturus viridescens were studied for DNA arrangement by polarized fluorescence microscopy and by linear dichroic ratio measurements. Intact chromosomes showed a small but negative polarization (?8%) of fluorescence, while the dichroic ratio was negative and quite appreciable (0.85). On treatment with trypsin or RNase the polarization value increased to about ?34% with no change in the polarization direction. The dichroic ratio on the other hand remained unchanged on such enzyme treatments. These results, along with the data of form dichroism and the change in fluorescence color following any enzyme action, suggest that basically the preexisting DNA arrangement was revealed by these enzymes. The fully enzyme-treated chromosome–dye complexes showed cross-bands. Quantitatively, the highest degree of DNA orientation across the above two chromosomes was in the range of 15–34%. This orientation fits well with a coiled coil-DNA, which is mostly longitudinal in these chromosomes. It is suggested that this longitudinal coil may have occasional defects in DNA structure. Alternatively, this coil may terminate into regions of random DNA and unsupercoiled DNA showing lateral projections, such as loops. This alternating feature of the DNA arrangement would tandemly repeat in either metaphase and lampbrush chromosomes.     

Size-dependent positioning of human chromosomes in interphase nuclei

By using a fluorescence in situ hybridization technique we revealed that for nine different q-arm telomere markers the positioning of chromosomes in human G(1) interphase nuclei was chromosome size-dependent. The q-arm telomeres of large chromosomes are more peripherally located than telomeres on small chromosomes. This highly organized arrangement of chromatin within the human nucleus was discovered by determining the x and y coordinates of the hybridization sites and calculating the root-mean-square radial distance to the nuclear centers in human fibroblasts. We demonstrate here that global organization within the G(1) interphase nucleus is affected by one of the most fundamental physical quantities-chromosome size or mass-and propose two biophysical models, a volume exclusion model and a mitotic preset model, to explain our finding.     

Non-random chromosome arrangement in triploid endosperm nuclei

The endosperm is at the center of successful seed formation in flowering plants. Being itself a product of fertilization, it is devoted to nourish the developing embryo and typically possesses a triploid genome consisting of two maternal and one paternal genome complement. Interestingly, endosperm development is controlled by epigenetic mechanisms conferring parent-of-origin-dependent effects that influence seed development. In the model plant Arabidopsis thaliana, we have previously described an endosperm-specific heterochromatin fraction, which increases with higher maternal, but not paternal, genome dosage. Here, we report a detailed analysis of chromosomal arrangement and association frequency in endosperm nuclei. We found that centromeric FISH signals in isolated nuclei show a planar alignment that may results from a semi-rigid, connective structure between chromosomes. Importantly, we found frequent pairwise association of centromeres, chromosomal segments, and entire arms of chromosomes in 3C endosperm nuclei. These associations deviate from random expectations predicted by numerical simulations. Therefore, we suggest a non-random chromosomal organization in the triploid nuclei of Arabidopsis endosperm. This contrasts with the prevailing random arrangement of chromosome territories in somatic nuclei. Based on observations on a series of nuclei with varying parental genome ratios, we propose a model where chromosomes associate pairwise involving one maternal and one paternal complement. The functional implications of this predicted chromosomal arrangement are discussed.     

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.     

Structure of human chromosomes studied by atomic force microscopy

In this work human chromosomes have been treated with RNase and pepsin to remove the layer of cellular material that covers the standard preparations on glass slides. This allows characterization of the topography of chromosomes at nanometer scale in air and in physiological solution by atomic force microscopy. Imaging of the dehydrated structure in air indicates radial arrangement of chromatin loops as the last level of DNA packing. However, imaging in liquid reveals a last level of organization consisting of a hierarchy of bands and coils. Additionally force curves between the tip and the chromosome in liquid are consistent with radial chromatin loops. These results and previous electron microscopy studies are analyzed, and a model is proposed for the chromosome structure in which radial loops and helical coils coexist.     

Arrangement of chromosomes in the interphase nucleus of plants

Chromosomal arrangement in the interphase nucleus has two main aspects: (1) arrangement of chromosomes with respect to nuclear polarity and to other nuclear components, and (2) arrangement of chromosomes with respect to one another. The latter aspect consists of two main types of spatial relationships; (a) relationships between different members of one chromosomal set, (b) relationships between different chromosomal sets. Data concerning various aspects of chromosomal arrangement in the interphase nucleus are presented and discussed and the genetic control as well as subcellular mechanisms which are involvled in nuclear organization, are elucidated. Evidence is presented indicating that, in common wheat, the gene system that determines the specific pattern of chromosomal arrangement in the nucleus is operating via the microtubular elements of the spindle system. The significance of ordered arrangement of chromosomes in the nucleus for the regularity of genetic activity and chromosomal behavior, is pointed out.Supported in part by a grant from the Stiftung Volkswagenwerk AZ I/34 075/76     

Electron microscopy of the parameres formed by the centromeric heterochromatin of human chromosome 9 at pachytene

The structure and arrangement of the parameres, which are small bodies representing part of the heterochromatin of human chromosome 9 at pachytene, were studied using transmission and scanning electron microscopy. Parameres appear to be denser than other parts of the chromosomes but have a similar fibrous substructure. The most common arrangement is clusters on the axis of the bivalent, consisting of varying numbers of parameres of variable size. The parameres are joined to each other and to the rest of the chromosome by interconnecting fibres. No evidence was obtained for the organisation of parameres into paired lateral loops, as proposed by previous workers using light microscopy. The combination of osmium impregnation of pachytene chromosomes with a backscattered electron detector in the scanning electron microscope produced very clear images of the pattern of chromomeres. This procedure may prove valuable for pachytene mapping of chromosomes because of the greatly improved resolution compared with light microscopy.     

The spatial distribution of chromosomes in metaphase neuroblast cells from subspecific F1 hybrids of the grasshopper Caledia captiva

The spatial distribution of chromosomes has been analysed in radial metaphase neuroblast cells in F₁ hybrid embryos generated by crossing individuals of the Moreton and Torresian (TT) chromosomal taxa of the grasshopper Caledia captiva. The Moreton individuals were of two kinds depending on whether they carried an acrocentric X (MAX) or a metacentric X (MMX). No significant associations were detected between any pair of homologous chromosomes in either male or female (MAX x TT) and (MMX x TT) F₁ hybrids. This result was supported by data which showed that the mean separation between homologues is greater, although not significantly so, than the mean separation between non-homologous chromosomes within the two Moreton genomes. Indeed, in a number of cases, genome separation was clearly observed in radial metaphase preparations from these F₁ hybrids. By comparison the analysis of pairwise associations between non-homologous chromosomes within the MMX and MAX Moreton genomes revealed a number of significant associations and dissociations which strongly suggests that at least some chromosomes in these genomes are organised non-randomly at metaphase. Of particular interest was the highly significant X-5 association in the MMX genome since in a previous study X-5 rearrangements were found to occur repeatedly among different backcross progeny involving Moreton x Torresian F₁ hybrids. Additionally a comparison of the organisation of chromosomes in the MAX and MMX genomes, which differ primarily by the type of X chromosome, revealed that in a number of cases pairs of chromosomes are arranged very differently with respect to each other. The distribution of chromosomes on the hollow spindle was also analysed to investigate whether a specific spatial ordering of chromosomes exists within these Moreton genomes based on the association of pairs of short arms and pairs of long arms of most similar length (the Bennett model). The twelve chromosomes in both genomes were uniquely ordered in a single chain. However, because of computing limitations, only the ordered arrangement of chromosomes 1–10 was investigated. An analysis of 48 cells in the MMX and 38 cells in the MAX genomes showed that the predicted order in the ten chromosome sub-set in each genome did not rank in the top 20% of the 181,440 possible orders. This suggests that, although there is a good evidence that some non-homologous chromosomes may be associated non-randomly at metaphase in these genomes, they do not appear to show a specific, ordered arrangement as predicted by the Bennett model. The significance of the observed non-random organisation of chromosomes in the MMX and MAX genomes is discussed in relation to the generation of novel chromosome rearrangements in Moreton x Torresian F₁ hybrids and the evolution of the Moreton and Torresian genomes.     

The spatial organization of the genome in mammalian cells

A number of recent studies have indicated that the location of a given mammalian chromosome within the interphase nucleus is related to its size, whereas other work has implicated a chromosome's gene density as a factor. Recent investigations of the degree to which an ordered arrangement of mitotic chromosomes on the metaphase plate is inherited and perpetuated during successive cell cycles have also yielded somewhat controversial results. The arrangement of chromosomes in the nucleus also has been investigated by the analysis of chromosomal translocations, with some surprising recent findings.     

Hierarchy of organization in eukaryotic chromosomes (a review)

Summary Several models of macromolecular arrangements in eukaryotic chromosomes have been proposed during the past fifteen years. Many of the models are consistent with physical and chemical data on the molecular components of chromosomes, and a few have the appearance of meeting the requirements for cytological organization in chromosomes. However, one of the most frustrating problems in developing a working model is to provide a scheme that fits genetic function while satisfying the structural parameters. This has not yet been achieved.Although emphasis in this review has been placed on uninemic and polynemic models, alternatives, such as a bineme, for example, remain. It is clear, moreover, that the issue can be resolved only through continued efforts to make direct observations of chromosomes with light and electron microscopy coupled with the additional tools ofX-ray analysis and analytical biochemistry. A recent analysis byWray andStubblefield (1969) has led to a rather innovative model of the chromosome, and exemplifies the kind of approach needed to clarify the phenomenon. Furthermore, analyses of meiotic chromosomes may provide valuable insight for relating organization to genetic function (cf Maguire, 1966 andBraselton, pers. comm). Of particular interest are mutation events as related to subchromatid organization, and the reorganization of chromosomal fibrils during early meiotic stages. At present, and as a generalization, the evidence points more strongly toward at least a binemic arrangement of chromosomal subunits than toward a uninemic one.     

The internal order of the interphase nucleus

Summary This paper has two parts. The first one is theoretical, whereas in the second, some experimenteal results are reported. Part 1: Theoretical Considerations. Comings' considerations on an ordered arrangement of chromatin in the interphase nucleus are used as a basis for further investigations and calculations in order to establish a preliminary model of the interphase nucleus. Information on the amount of DNA of a diploid human nucleus, on the degree of spiralization of chromatin threads found in electron microscopy, and measurements of salivary gland chromosomes was used to estimate the lengths of the entire interphase chromosomes. The number of fixing points-pores—was indirectly calculated proposing a model of an internal order of the chromatin threads. This number was found in concord with a direct calculation of the number of pores in the nuclear membrane based on results from electron microscopy. Part 2: Experimental Results and Discussion. In the second part of this study, an approach was made as to how to arrange chromosomes and chromosome segments in their proximity to each other. Results of cytogenetic studies of newborn babies and abortions, of cells from patients with Bloom's syndrome and Fanconi's anemia and normal cells treated with Mitomycin C and Trenimon, are thought to be informative under certain suppositions for the problem, which chromosome or chromosome parts are situated in proximity to each other. The symmetrical and equal interchanges seen, for example, in Bloom's syndrome are an indication of somatic pairing during the time of reunion. Therefore, the unequal interchanges in the same syndrome in which different chromosomes are involved should give evidence for proximity of nonhomologous chromosomes. Arguments for and against a temporal and spacial hypothesis for somatic pairing are discussed. The differing frequencies of chromosomes involved in Robertsonian translocations in man are informative for proximities of satellite regions at the nucleolus. Nucleolus and sex chromatin could be used as fixed points in a model of the interphase nucleus in which finally the absolute localization of the chromosomes will be discovered. The discussion points out promising methods for further investigations on the subject and mentions problems which could be attacked if the approach described here leads to a model of internal order in the interphase nucleus.This work was supported by the Deutsche Forschungsgemeinschaft within the Sonderforschungsbereich 35, Klinische Genetik.     

Interphase chromosome arrangement in Anopheles atroparvus

The arrangement of chromosomes in interphase nuclei of Anopheles atroparvus has been inferred from an analysis of: 1. The early stages of mitosis as seen following Quinacrine staining, and 2. The reversible effects on the chromatin pattern obtained following the treatment of living cells with various NaCl solutions, and the following conclusions have been reached: (a) The chromatin is connected to the nuclear membrane, (b) Homologous chromosomes show close side-by-side somatic pairing, (c) The long arms of the sex chromosomes form a fluorescent peripheral body, (d) The autosomes are strongly reflexed at the centromeres, (e) The autosomal centromeric regions are polarized towards the peripheral body, (f) The telomeric regions of all the autosomes are closely apposed.--A ring-shaped pattern of interphase chromatin is constantly and reversibly induced by NaCl 0.15 to 0.18 M solutions.--These relationships indicate a peripheral arrangement of the interphase somatic complement.--The distribution of the chromosomes in polytene nuclei and at the beginning of meiosis resembles that suggested above for somatic interphase cells. This distribution may apply more widely in the Diptera.     

Orientation and segregation of a micromanipulated multivalent: Familiar principles,divergent outcomes

We studied the orientation and segregation of a particular quadrivalent in living grasshopper spermatocytes. Quadrivalents were detached from the spindle by micromanipulation, then placed and bent as desired. The detached quadrivalents reattach and orient on the spindle. Their orientation is determined by the same principles that apply to ordinary chromosomes in mitosis and meiosis, but the outcome is different. Certain characteristics of the quadrivalent lead to a variety of orientations rather than the single one typical of ordinary chromosomes. Two kinetochores in the quadrivalent are linked to the others by unusually long, flexible chromosome arms. These kinetochores may face either the same pole or opposite poles and tend to orient initially to the pole toward which they face. Consequently, the initial orientation of the flexibly linked kinetochores is variable, and, moreover, they frequently reorient. In contrast, the other two kinetochores are as rigidly connected as those in a small bivalent and so display the typical back-to-back arrangement. Usually, this arrangement leads quickly to a stable orientation of the two kinetochores to opposite poles. Sometimes, however, the back-to-back arrangement changes to a side-by-side arrangement so that the orientation of both kinetochores to the same pole is favored. The combined effect of this diverse behavior is that the quadrivalent has four stable orientations, each leading to a different distribution of chromosomes in anaphase. The result is genetic chaos. Ironically, this chaos is produced by the same mechanisms that, in ordinary bivalents and mitotic chromosomes, produce a single stable orientation and genetically appropriate chromosome distribution.by P.B. Moens     

Random arrangement of chromosomes in a radial metaphase configuration

During metaphase II of spermatogenesis the chromosomes of the grasshopper, Melanoplus femurrubrum (De Geer), are arranged at the periphery of the metaphase plate in what has been termed the radial metaphyse configuration. Cells at this stage contain two long, three short, and either six or seven chromosomes of medium length. The arrangement of the chromosomes in the metaphase plate was analyzed by counting the number of medium-sized chromosomes which separated the two long chromosomes. In the 351 cells analyzed the frequencies of cells with the various types of arrangements agreed closely with those expected from a random arrangement of the chromosomes in the metaphase plate. The possible role of chromosome-to-chromosome connectives in the arrangement of the chromosomes in the radial configuration is discussed.Supported by Grant GB 23665 from the National Science Foundation Washington, D.C.     

Alternative ends: telomeres and meiosis

Meiosis is a specialized type of cell division that halves the diploid number of chromosomes, yielding four haploid nuclei. Dramatic changes in chromosomal organization occur within the nucleus at the beginning of meiosis which are followed by the separation of homologous chromosomes at the first meiotic division. This is the case for telomeres that display a meiotic-specific behavior with gathering in a limited sector of the nuclear periphery. This leads to a characteristic polarized chromosomal configuration, called the "bouquet" arrangement. The widespread phenomenon of bouquet formation among eukaryotes has led to the hypothesis that it is functionally linked to the process of interactions between homologous chromosomes that are a unique feature of meiosis and are essential for proper chromosome segregation. Various studies in different model organisms have questioned the role of the telomere bouquet in chromosome pairing and recombination, and very recently in meiotic spindle formation, and have provided some clues about the molecular mechanisms that carry out this specific clustering of telomeres.     

Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds

At a resolution of 850 bands, human chromosomes comprise two subsets of bands, the GC-richest H3⁺ and the GC-poorest L1⁺ bands, accounting for about 17 and 26%, respectively, of all bands. The former are a subset of the R bands and the latter are a subset of the G bands. These bands showed the highest and the lowest gene densities, respectively, as well as a number of other distinct features. Here we report that human and chicken interphase nuclei are characterized by the following features. (1) The gene-richest/GC-richest chromosomal regions are predominantly distributed in internal locations, whereas the gene-poorest/GC-poorest DNA regions are close to the nuclear envelope. (2) The interphase chromosomes seem to be characterized by a polar arrangement, because the gene-richest/GC-richest bands and the gene-poorest/GC-poorest bands are predominantly located in the distal and proximal regions, respectively, of chromosomes, and because interphase chromosomes are extremely long. While this polar arrangement is evident in the larger chromosomes, it is not displayed by the chicken microchromosomes and by some small human chromosomes, namely by chromosomes that are almost only composed by GC-rich or by GC-poor DNA. (3) The gene-richest chromosomal regions display a much more spread-out conformation compared to the gene-poorest regions in human nuclei. This finding has interesting implications for the formation of GC-rich isochores of warm-blooded vertebrates.     

Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes

Chromatin organization is central to many conserved biological processes, but it is generally unknown how the underlying nucleosomes are arranged in situ. Here, we have used electron cryotomography to study chromatin in the picoplankton Ostreococcus tauri, the smallest known free-living eukaryote. By visualizing the nucleosome densities directly, we find that O. tauri chromosomes do not arrange into discrete, compact bodies or any other higher level of order. In contrast to the textbook 30-nm fiber model, O. tauri chromatin resembles a disordered assemblage of nucleosomes akin to the polymer melt model. This disorganized nucleosome arrangement has important implications for potentially conserved functions in tiny eukaryotes such as the clustering of nonhomologous chromosomes at the kinetochore during mitosis and the independent regulation of closely positioned adjacent genes.     

The ordered arrangement of chromosomes in the Chinese hamster spermatocyte nucleus

Summary The question of chromosome distribution in the mammalian nucleus is addressed, and data are provided in support of the ordered arrangement of chromosomes in the Chinese hamster spermatocyte. Testicular cells were dispersed and air-dried without prior fixation, then stained and karyotyped. The position of chromosome telomeres in 217 pachytene spermatocytes was determined in relation to four concentric rings which equally divided the nuclear area. The distribution of telomeres showed a progressive decline from the central to the peripheral rings. This was particularly pronounced for chromosomes 1–7, but was reversed for the XY chromosomes. The distribution of the total as well as of the individual chromosomes was significantly different from that expected on the basis of random distribution. The only exceptions to this were chromosomes 8–10, which exhibited random distribution. Thus, while chromosomes 1–7 had a central position, the XY pair had a peripheral localization. The mean ring position appeared to be related to chromosome length, except for the XY chromosomes, suggesting that chromosome length may determine chromosome position.     

Die Speicheldrüsenchromosomen der StechmückeCulex pipiens L. II. Ergänzungen zur Kartierung

The map of larval salivary gland chromosomes of the mosquitoCulex pipiens L. is amended as follows: The banding pattern is corrected in arm 1L, and completed in 2L. The amendments were verified on isolated entire chromosomes. Discrepancies between the three maps published previously, are ascribed to differences in method of the respective authors. In map collation, only well-spread chromosomes of a similar degree of polyteny should be used. The spatial arrangement of chromosomes in the nucleus is discussed, and indications are given for distinguishing between chromosome ends and accidental breaks.