In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

Ultrastructural Details of Mammalian Chromosome Architecture

Over the past decade, 3C-related methods have provided remarkable insights into chromosome folding in vivo. To overcome the limited resolution of prior studies, we extend a recently developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts. Micro-C robustly captures known features of chromosome folding including compartment organization, topologically associating domains, and interactions between CTCF binding sites. In addition, Micro-C provides a detailed map of nucleosome positions and localizes contact domain boundaries with nucleosomal precision. Compared to Hi-C, Micro-C exhibits an order of magnitude greater dynamic range, allowing the identification of ∼20,000 additional loops in each cell type. Many newly identified peaks are localized along extrusion stripes and form transitive grids, consistent with their anchors being pause sites impeding cohesin-dependent loop extrusion. Our analyses comprise the highest-resolution maps of chromosome folding in human cells to date, providing a valuable resource for studies of chromosome organization.

Fbxo30 regulates chromosome segregation of oocyte meiosis

As the female gamete, meiotic oocytes provide not only half of the genome but also almost all stores for fertilization and early embryonic development. Because de novo mRNA transcription is absent in oocyte meiosis, protein-level regulations, especially the ubiquitin proteasome system, are more crucial. As the largest family of ubiquitin E3 ligases, Skp1-Cullin-F-box complexes recognize their substrates via F-box proteins with substrate-selected specificity. However, the variety of F-box proteins and their unknown substrates hinder our understanding of their functions. In this report, we find that Fbxo30, a new member of F-box proteins, is enriched in mouse oocytes, and its expression level declines substantially after the metaphase of the first meiosis (MI). Notably, depletion of Fbxo30 causes significant chromosome compaction accompanied by chromosome segregation failure and arrest at the MI stage, and this arrest is not caused by over-activation of spindle assembly checkpoint. Using immunoprecipitation and mass spectrometric analysis, we identify stem-loop-binding protein (SLBP) as a novel substrate of Fbxo30. SLBP overexpression caused by Fbxo30 depletion results in a remarkable overload of histone H3 on chromosomes that excessively condenses chromosomes and inhibits chromosome segregation. Our finding uncovers an unidentified pathway-controlling chromosome segregation and cell progress.

Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq)

The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives have contributed tremendously to the now widely accepted view that genome topology plays an important role in many major cellular processes, at a chromosome-wide scale, but certainly also at the level of individual genetic loci. A particularly popular application of 3C technology is to study transcriptional regulation, allowing researchers to draw maps of gene regulatory connections beyond the linear genome through addition of the third dimension. In this chapter, we provide a highly detailed protocol describing 3C coupled to high-throughput sequencing (referred to as 3C-Seq or more commonly 4C-Seq), allowing the unbiased interrogation of genome-wide chromatin interactions with specific genomic regions of interest. Interactions between spatially clustered DNA fragments are revealed by crosslinking the cells with formaldehyde, digesting the genome with a restriction endonuclease and performing a proximity ligation step to link interacting genomic fragments. Next, interactions with a selected DNA fragment are extracted from the 3C library through a second round of digestion and ligation followed by an inverse PCR. The generated products are immediately compatible with high-throughput sequencing, and amplicons from different PCR reactions can easily be multiplexed to dramatically increase throughput. Finally, we provide suggestions for data analysis and visualization.

Thioredoxin-interacting protein regulates glucose metabolism and affects cytoplasmic streaming in mouse oocytes

Thioredoxin-interacting protein (Txnip) regulates intracellular redox state and prompts oxidative stress by binding to and inhibiting Thioredoxin (Trx). In addition, via a Trx-independent mechanism, Txnip regulates glucose metabolism and thus maintains intracellular glucose levels. Previously, we found Txnip mRNA highly expressed in immature germinal vesicle (GV) oocytes, but currently there is no report describing the role of Txnip in oocytes. Therefore, we conducted the present study to determine the function of Txnip in mouse oocytes' maturation and meiosis by using RNA interference (RNAi) method. Upon specific depletion of Txnip, 79.5% of oocytes were arrested at metaphase I (MI) stage. Time-lapse video microscopy analysis revealed that the formation of granules in the oocyte cytoplasm increased concurrent with retarded cytoplasmic streaming after Txnip RNAi treatment. Txnip RNAi-treated oocytes had upregulated glucose uptake and lactate production. To confirm the supposition that mechanism responsible for these observed phenomena involves increased lactate in oocytes, we cultured oocytes in high lactate medium and observed the same increased granule formation and retarded cytoplasmic streaming as found by Txnip RNAi. The MI-arrested oocytes exhibited scattered microtubules and aggregated chromosomes indicating that actin networking was disturbed by Txnip RNAi. Therefore, we conclude that Txnip is a critical regulator of glucose metabolism in oocytes and is involved in maintaining cytoplasmic streaming in mouse oocytes.

[Racial and population variability of phenotypic (cranial) characters in the common shrew Sorex araneus L., 1758]

Variability of the cranial properties of chromosomal races Serov, Manturovo and Pechora of the common shrew were studied. A consistent increase of scull size in the Serov race with moving from the plain to highlands and a skull size decrease from low to high latitudes was detected. Interpopulation variability among different races was shown to be comparable with interracial variability or to exceed it. This suggests microevolution at the level of local populations.

Model of chromosome associations in Mus domesticus spermatocytes

Understanding the spatial organization of the chromosomes in meiotic nuclei is crucial to our knowledge of the genome's functional regulation, stability and evolution. This study examined the nuclear architecture of Mus domesticus 2n=40 pachytene spermatocytes, analyzing the associations among autosomal bivalents via their Centromere Telomere Complexes (CTC). The study developed a nuclear model in which each CTC was represented as a 3D computer object. The probability of a given combination of associations among CTC was estimated by simulating a random distribution of 19 indistinguishable CTC over n indistinguishable "cells" on the nuclear envelope. The estimated association frequencies resulting from this numerical approach were similar to those obtained by quantifying actual associations in pachytene spermatocyte spreads. The nuclear localization and associations of CTC through the meiotic prophase in well-preserved nuclei were also analyzed. We concluded that throughout the meiotic prophase: 1) the CTC of autosomal bivalents are not randomly distributed in the nuclear space; 2) the CTC associate amongst themselves, probably at random, over a small surface of the nuclear envelope, at the beginning of the meiotic prophase; 3) the initial aggregation of centromere regions occurring in lepto-zygotene likely resolves into several smaller aggregates according to patterns of preferential partitioning; 4) these smaller aggregates spread over the inner face of the nuclear envelope, remaining stable until advanced stages of the meiotic prophase or even until the first meiotic division.

[The structure of long telomeres in chromosomes of the Iberian shrew]

It is shown that the size, localization, and structure of telomeres in the Iberian shrew (Sorex granarius) are not characteristic of mammals. In this species, long telomeres of an average size of 213 kb are localized on the short arms of all 32 acrocentrics; ribosomal blocks and active nucleolus-organizing regions (NORs) were also discovered there. At the remaining chromosome ends the average size of telomeres is 3.8 kb. However, in a closely related species, Sorex araneus, all telomeres have size similar to that of human telomeres, i.e., 6.8-15.2 kb. Despite the fact that some long telomeres contain ribosomal repeats in addition to telomeric ones, the long telomeres have preserved asymmetry of G- and C-rich strands as in functional telomeres. It is probable that long telomeres were formed in meiosis at the stage of chromosome bouquet as a result of global reorganization of the chromosome ends. The provoking factors for such reorganization might be the fission of several metacentrics and the necessity of telomerization of the resulting acrocentrics.

[The role of chromosome rearrangements in evolution of mole voles of genus Ellobius (Rodentia, Mammalia)]

Modern mole voles of the genus Ellobius are characterized by species-specific features of autosomes and sex chromosomes. Owing to the use of the Zoo-FISH method, the nomenclature of chromosomes was refined and nonhomologous Robertsonian translocations indistinguishable by G-staining were identified for Ellobius tancrei, which is a species with a wide chromosome variation of the Robertsonian type. The electron-microscopic analysis of synaptonemal complexes in F1 hybrids of forms with 2n = 50 and 2n = 48 revealed the formation of a closed SC-pentavalent composed of three metacentrics with monobrachial homology and two acrocentrics. Segregation of chromosomes of such complex systems is impeded by disturbances in the nucleus architecture leding to the formation of unbalanced gametes and to a dramatic reduction in fertility of hybrids. Our data support the hypothesis that the formation of monobrachial homologous metacentric chromosomes can be considered as a way of chromosomal speciation.

Inverted nuclear architecture and its development during differentiation of mouse rod photoreceptor cells: a new model to study nuclear architecture

Interphase nuclei have a conserved architecture: heterochromatin occupies the nuclear periphery, whereas euchromatin resides in the nuclear interior. It has recently been found that rod photoreceptor cells of nocturnal mammals have an inverted architecture, which transforms these nuclei in microlenses and supposedly facilitates a reduction in photon loss in the retina. This unique deviation from the nearly universal pattern throws a new light on the nuclear organization. In the article we discuss the implications of the studies of the inverted nuclei for understanding the role of the spatial organization of the nucleus in nuclear functions.

[Nuclear matrix organization of the chromocenters in cultured murine fibroblasts]

In the current work, the structural organization of nuclear matrix of pericentromeric heterochromatin blocks (chromocenters) inside cultured murine fibroblasts was investigated. After 2 M NaCl extraction without DNase I treatment, chromocenters were extremely swelled, and it was impossible to detect them using conventional electron microscopy. Using immunogolding with anti-topoisomerase IIalpha antibody, we demonstrated that residual chromocenters were subdivided into numerous discrete aggregates. After 2 M NaCl extraction with DNase I treatment, the residual chromocenters appeared as a dense meshwork of thin fibers, and using this feature, the residual chromocenters were easily distinguished from the rest of nuclear matrix. After extraction with dextran sulfate and heparin, the chromocenters were decondensed, and chromatin complexes having rosette organization (central core from which numerous DNA fibers radiated) were seen. Probably, the appearance of these rosettes was a consequence of incomplete chromatin extraction. Thus, the nuclear matrix of pericentromeric chromosome regions in cultured murine fibroblasts differs morphologically from the rest of nuclear matrix.

Chromosome shattering: a mitotic catastrophe due to chromosome condensation failure

Chromosome shattering has been described as a special form of mitotic catastrophe, which occurs in cells with unrepaired DNA damage. The shattered chromosome phenotype was detected after application of a methanol/acetic acid (MAA) fixation protocol routinely used for the preparation of metaphase spreads. The corresponding phenotype in the living cell and the mechanism leading to this mitotic catastrophe have remained speculative so far. In the present study, we used V79 Chinese hamster cells, stably transfected with histone H2BmRFP for live-cell observations, and induced generalized chromosome shattering (GCS) by the synergistic effect of UV irradiation and caffeine posttreatment. We demonstrate that GCS can be derived from abnormal mitotic cells with a parachute-like chromatin configuration (PALCC) consisting of a bulky chromatin mass and extended chromatin fibers that tether centromeres at a remote, yet normally shaped spindle apparatus. This result hints at a chromosome condensation failure, yielding a "shattered" chromosome complement after MAA fixation. Live mitotic cells with PALCCs proceeded to interphase within a period similar to normal mitotic cells but did not divide. Instead they formed cells with highly abnormal nuclear configurations subject to apoptosis after several hours. We propose a factor depletion model where a limited pool of proteins is involved both in DNA repair and chromatin condensation. Chromosome condensation failure occurs when this pool becomes depleted.

Analyzing mammalian female meiosis

The goal of this chapter is twofold: First, to acquaint the reader with the problems inherent in analyzing mammalian female meiosis and, second, to provide a step-by-step approach to mastering the necessary techniques. Although the methods presented are for use in the human and mouse, with subtle alterations the same techniques should be applicable to most mammalian species.

Cryotops versus open-pulled straws (OPS) as carriers for the cryopreservation of bovine oocytes: effects on spindle and chromosome configuration and embryo development

Two experiments were designed to assess the effectiveness of cryopreserving bovine MII oocytes using cryotops as the carrier system for vitrification. In the first experiment, we examined the developmental competence of oocytes after: (i) vitrification in open-pulled straws (OPS method); or (ii) vitrification in <0.1mul medium droplet on the surface of a specially constructed fine polypropylene strip attached to a plastic handle (Cryotop method). In the second experiment, warmed oocytes that had been vitrified in OPS or cryotops were fixed to analyze spindle and chromosome configuration. In all experiments both cow and calf oocytes were used. Significantly different fertilization rates were observed between the vitrification groups: 31.5% and 20.2% for the cow and calf oocytes vitrified in OPS, respectively, versus 46.1% and 46.4% for the oocytes vitrified using cryotops. After in vitro fertilization, 3.8% of the calf oocytes and 5.3% of the cow oocytes developed to the blastocyst stage. All blastocysts from vitrified oocytes resulted from the Cryotop method. A significantly lower percentage of the OPS-vitrified calf oocytes showed a normal spindle configuration (37.8%) compared to control fresh oocytes (69.9%), while normal spindle and chromosome configurations were observed in a significantly higher proportion of the cryotop-vitrified calf oocytes (60.2%). For the cow oocytes, 60.6% in the OPS group and 60.3% in the Cryotop group exhibited a normal morphology after warming. These findings suggest the cryotop system is a more efficient carrier for vitrification than OPS for the cryopreservation of bovine oocytes.

[The status of nucleolus organizing regions in hybrids of pluripotent and somatic mouse cells cultured under different conditions]

In the present work we examined the status of nucleolus organizing regions of mitotic chromosomes (NOR) in hybrid cells obtained by fusion of the mouse teratocarcinoma cells PCC4aza1 and adult mouse spleenocytes upon cultivation of hybrid cells under different conditions. We have shown that extended cultivation of hybrid cells in medium supplemented with HAT (hypoxanthine, aminopterin, thymidine) promotes the maintenance of NO-chromosomes, whereas under nonselective conditions elimination of NO-chromosome occurs. In nonselective medium the number of active, i. e. Ag-positive, NORs has been augmented comparatively to that observed under selective conditions. This observation directly indicates that reprogramming of the parental cell genomes in hybrid cells includes changes in the status of chromosomal NORs. The number of active NORs depends on conditions of hybrid cells culturing and may be changed by either of the two major ways--by elimination of NO-chromosomes (under nonselective conditions) or by inactivation of some NORs, when the general number of NO-chromosomes remains unaltered (under selective conditions).

Condensin I reveals new insights on mouse meiotic chromosome structure and dynamics

Chromosome shaping and individualization are necessary requisites to warrant the correct segregation of genomes in either mitotic or meiotic cell divisions. These processes are mainly prompted in vertebrates by three multiprotein complexes termed cohesin and condensin I and II. In the present study we have analyzed by immunostaining the appearance and subcellular distribution of condensin I in mouse mitotic and meiotic chromosomes. Our results demonstrate that in either mitotically or meiotically dividing cells, condensin I is loaded onto chromosomes by prometaphase. Condensin I is detectable as a fuzzy axial structure running inside chromatids of condensed chromosomes. The distribution of condensin I along the chromosome length is not uniform, since it preferentially accumulates close to the chromosome ends. Interestingly, these round accumulations found at the condensin I axes termini colocalized with telomere complexes. Additionally, we present the relative distribution of the condensin I and cohesin complexes in metaphase I bivalents. All these new data have allowed us to propose a comprehensive model for meiotic chromosome structure.

Effect of vitrification solutions and cooling upon in vitro matured prepubertal ovine oocytes

The vitrification procedure effects on molecular and cytoskeletal components and on developmental ability of in vitro matured prepubertal ovine oocytes were evaluated. MII oocytes were divided into three groups: (1) vitrified in cryoloops (VTR); (2) exposed to vitrification solutions and rehydrated without being plunged into liquid nitrogen (EXP); (3) without further treatment as a control (CTR). Two hours after treatment, membrane integrity, assessed by propidium iodide/Hoechst staining, was lower in VTR and EXP than in CTR (70.6%, 88.5% and 95.2%, respectively). Cleavage rate after fertilization was statistically different among all groups (21.4%, 45.4% and 82.8% for VTR, EXP and CTR groups respectively; P<0.01). Blastocyst rate in VTR (0.0%) and EXP (2.8%) groups was lower (P<0.01) than in CTR (22.8%). Maturation promoting factor activity was lower (P<0.01) in VTR and EXP groups compared with CTR at both 0 h (82.2%, 83.6% and 100%, respectively) and 2 h (60% and 53.9% and 100%, respectively) after warming. Immediately after warming VTR and EXP oocytes showed a lower rate of normal spindle and chromosome configuration compared to CTR (59.1%, 48.0% and 83.3%, respectively; P<0.01). After 2 h of culture in standard conditions the percentage of oocytes with normal spindle and chromosome organization decreased in both VTR and EXP groups compared to CTR (36.4%, 42.8% versus 87.5%, respectively). In conclusion the exposition to the tested cryoprotectant solution and the vitrification in cryoloops modified cytoskeletal components and alter biochemical pathways that compromise the developmental capacity of prepubertal in vitro matured ovine oocytes.

Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation

The relocalisation of some genes to positions outside chromosome territories, and the visible decondensation or unfolding of interphase chromatin, are two striking facets of nuclear reorganisation linked to gene activation that have been assumed to be related to each other. Here, in a study of nuclear reorganisation around the Hoxd cluster, we suggest that this may not be the case. Despite its very different genomic environment from Hoxb, Hoxd also loops out from its chromosome territory, and unfolds, upon activation in differentiating embryonic stem (ES) cells and in the tailbud of the embryo. However, looping out and decondensation are not simply two different manifestations of the same underlying change in chromatin structure. We show that, in the limb bud of the embryonic day 9.5 embryo,where Hoxd is also activated, there is visible decondensation of chromatin but no detectable movement of the region out from the chromosome territory. During ES cell differentiation, decondensed alleles can also be found inside of chromosome territories, and loci that have looped out of the territories can appear to still be condensed. We conclude that evolutionarily conserved chromosome remodelling mechanisms, predating the duplication of mammalian Hox loci, underlie Hox regulation along the rostrocaudal embryonic axis. However, we suggest that separate modes of regulation can modify Hoxd chromatin in different ways in different developmental contexts.

Condensation of Interphase Chromosomes in Nuclei of Synchronized CHO Cells

The escape of individual interphase chromosomes from nuclei of reversibly permeabilized Chinese hamster ovary (CHO) cells was utilized for the visualization of condensing interphase chromosomes in a cell cycle-dependent manner in synchronized cells. Major interphase chromosomal forms include: (a) mid-S-phase globular chromosomes at 3.0 C-value, (b) late mid-S-phase fibrous hemicircular forms (3.3 C), (c) late-S-phase supercoiled ribbons (3.7 C), and (d) end-S-phase elongated, bent prechromosomal structures (4.0 C).

Mitosis: disorderly conduct at the kinetochore

Conventional models posit that microtubules bound to kinetochores act coordinately during chromosome movement. Such models need to be revised in the light of new data demonstrating uncoordinated behavior among kinetochore-associated microtubules.

Atomic force microscope tracking observation of Chinese hamster ovary cell mitosis

CHO cells possess easily identifiable karyotypes, and CHO cell chromosomes are large and few in number, making these cells ideal for mutational and drug toxicity studies and suitable for investigations of animal chromosome structure. Here, we used atomic force microscopy (AFM) in the tapping mode for detailed visualizations of Chinese hamster ovary (CHO) cell chromosomes during various mitotic phases, including typical prophase, prometaphase, metaphase, anaphase and telophase. Based on our detailed observations, we were able to divide metaphase and anaphase into sub-phases: metaphase I, II and III, and anaphase I and II. Furthermore, we used the AFM error-signal mode to visualize chromosomal ultrastructures and cytokinesis. While these visualizations were all successful, we found that the image quality was affected by cellular debris, contamination. Collectively, our results show that the AFM technique has great potential for the detailed study of chromosomes and chromosomal ultrastructures during all phases of the cell cycle, but that careful standards of sample preparation must be maintained.

Genetic characterization of CHO production host DG44 and derivative recombinant cell lines

The dihydrofolate reductase-deficient Chinese hamster ovary (CHO) cell line DG44 is the dominant mammalian host for recombinant protein manufacturing, in large part because of the availability of a well-characterized genetic selection and amplification system. However, this cell line has not been studied at the cytogenetic level. Here, the first detailed karyotype analysis of DG44 and several recombinant derivative cell lines is described. In contrast to the 22 chromosomes in diploid Chinese hamster cells, DG44 has 20 chromosomes, only seven of which are normal. In addition, four Z group chromosomes, seven derivative chromosomes, and 2 marker chromosomes were identified. For all but one of the 16 DG44-derived recombinant cell lines analyzed, a single integration site was detected by fluorescence in situ hybridization regardless of the gene delivery method (calcium phosphate-DNA coprecipitation or microinjection), the topology of the DNA (circular or linear), or the integrated plasmid copy number (between 1 and 51). Chromosomal aberrations, observed in more than half of the cell lines studied, were mostly unbalanced with examples of aneuploidy, deletions, and complex rearrangements. The results demonstrate that chromosomal aberrations are frequently associated with the establishment of recombinant CHO DG44 cell lines. Noteworthy, there was no direct correlation between the stability of the genome and the stability of recombinant protein expression.

Chromosomes can congress to the metaphase plate before biorientation

The stable propagation of genetic material during cell division depends on the congression of chromosomes to the spindle equator before the cell initiates anaphase. It is generally assumed that congression requires that chromosomes are connected to the opposite poles of the bipolar spindle ("bioriented"). In mammalian cells, we found that chromosomes can congress before becoming bioriented. By combining the use of reversible chemical inhibitors, live-cell light microscopy, and correlative electron microscopy, we found that monooriented chromosomes could glide toward the spindle equator alongside kinetochore fibers attached to other already bioriented chromosomes. This congression mechanism depended on the kinetochore-associated, plus end-directed microtubule motor CENP-E (kinesin-7).

Interactions of the meiotic spindle with mitotic chromosomes in GV mouse oocytes

During mitosis, a spindle checkpoint detects chromosome misalignment and halts the cell cycle progression. In meiosis of female germ cells, however, it is debatable whether such a checkpoint is present. This research employed a unique model in the mouse, mitotic chromosomes transferred to meiotic cytoplasts to investigate whether a meiotic oocyte's microtubule apparatus can effectively separate mitotic metaphase chromosomes, and whether a spindle checkpoint exists during its division. The intact germinal vesicle (GV) oocytes, enucleated GV cytoplasts, and enucleated GV cytoplasts at 15 h in-vitro maturation were transferred with a metaphase fibroblast cell. When mitotic chromosomes were transferred into enucleated or intact mouse GV oocytes, the first bipolar meiotic spindles were established and the reconstructed oocytes were able to extrude polar bodies. However, none of the reconstructed oocytes showed complete and accurate alignment of chromosomes, except the enucleated GV cytoplasts reconstructed after maturation. The spindle formation and polar body extrusion suggest that the first meiotic spindle was functional, and the chromosome misalignment did not prevent the onset of anaphase. The data indicate that a spindle checkpoint, providing surveillance of misaligned chromosomes, was overridden or compromised by the incompatibility between somatic chromosomes and meiotic spindles during the first meiotic division.

[Experimental visualization of chromoneme as one of the higher levels of chromatin compactization in the mitotic chromosome]

We succeeded to visualize the chromoneme or a filamentous chromatin structure, with the mean thickness 0.1-0.2 microm, as a higher level of chromatin compactization in animal and plant cells at different stages of chromosome condensation at mitotic prophase and during chromatid decondensation at telophase. Under the natural conditions, chromoneme elements are not detected in the most condensed chromatin of metaphase chromosomes on ultrathin sections. We studied the ultrastructure and behavior of the chromatin of mitotic chromosomes in situ in cultured mouse L-197 cells under the conditions selectively demonstrating the chromoeneme structure of the mitotic chromosomes in the presence of Ca2+. Loosely packaged dense chromatin bands, ca. 100 nm in diameter, chromonemes, were detected in chromosome arms in a solution containing 3 mM CaCl2. When transferred in a hypotonic solution containing 10 mM tris-HCl, these chromosome swelled, lost the chromoneme level of structure, and rapidly transformed in loose aggregates of elementary DNP fibrils, 30 nm in diameter. After this decondensation in the low ionic strength solution, the chromoneme structure of mitotic chromosomes was restored when they were transferred in a Ca2+ containing solution. The morphological characteristics of the chromoneme and pattern of its packaging in the chromosome were preserved. However, when the mitotic cells with chromosomes, in which the chromoneme structure was visualized with the help of 3 mM CaCl2, were treated with a photosensbilizer, ethidium bromide, and illuminate with a light with the wavelength 460 nm, chromatic decondensation under the hypotonic solution was not observed. The chromoneme elements in a stabilized chromatin of the mitotic chromosome preserved specific interconnection and their general pattern of packaging in in the chromatic was also preserved. The chromoneme elements in the chromosomes stabilized by light preserved their density and diameter even in a 0.6 M NaCl solution, which normally leads to chromoneme destruction. An even more rigid treatment of the stabilized chromosomes with a 2 M NaCl solution, which normally fully decondenses the chromosomes, made it possible to detect a 3D reticular skeleton devoid of any axial structures.

Microdissection-derived murine mcb probes from somatic cell hybrids

The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes.

Non-invasive method to assess genotoxicity of nocodazole interfering with spindle formation in mammalian oocytes

Trisomies due to nondisjunction in oogenesis are still a major cause of genetic diseases in humans. In this study, we analysed spindle morphology of in vitro matured nocodazole-exposed mouse oocytes by novel non-invasive Polscope-microscopy, and compared images to those obtained by anti-tubulin immunofluorescence of fixed oocytes. Polscope revealed a reduction in the numbers of oocytes expressing a birefringent spindle, and alterations in spindle morphology at concentrations of nocodazole below those inducing detectable aberrations in immunofluorescence. Hyperploidy increased significantly at a concentration of 40 nM nocodazole in mouse metaphase II oocytes, similar to thresholds inducing nondisjunction in cultured human lymphocytes. In conclusion, Polscope represents a novel highly sensitive, non-invasive method to identify chemicals inducing severe spindle aberrations that predispose mammalian oocytes to nondisjunction. Polscope may provide information on the functionality of the spindle in experimental studies but is also compatible with clinical trials in human assisted reproduction due to its non-invasive nature.

A mitotic septin scaffold required for Mammalian chromosome congression and segregation

Coordination of cytokinesis with chromosome congression and segregation is critical for proper cell division, but the mechanism is unknown. Here, septins, a conserved family of polymerizing guanosine triphosphate-binding proteins, localized to the metaphase plate during mitosis. Septin depletion resulted in chromosome loss from the metaphase plate, lack of chromosome segregation and spindle elongation, and incomplete cytokinesis upon delayed mitotic exit. These defects correlated with loss of the mitotic motor and the checkpoint regulator centromere-associated protein E (CENP-E) from the kinetochores of congressing chromosomes. Mammalian septins may thus form a mitotic scaffold for CENP-E and other effectors to coordinate cytokinesis with chromosome congression and segregation.

Number and nuclear localisation of nucleoli in mammalian spermatocytes

In seven mammalian species, including man, the position and number of nucleoli in pachytene spermatocyte nuclei were studied from electron microscope (EM) nuclear sections or bivalent microspreads. The number and position of the nucleolar organiser regions (NORs) in mitotic and meiotic chromosomes were also analysed, using silver staining techniques and in situ hybridisation protocols. The general organisation of pachytene spermatocyte nucleoli was almost the same, with only minor morphological differences between species. The terminal NORs of Thylamys elegans (Didelphoidea, Marsupialia), Dromiciops gliroides (Microbiotheridae, Marsupialia), Phyllotys osgoodi (Rodentia, Muridae) and man, always gave rise to peripheral nucleoli in the spermatocyte nucleus. In turn, the intercalated NORs from Octodon degus, Ctenomys opimus (Rodentia, Octodontidae) and Chinchilla lanigera (Rodentia, Cavidae), gave rise to central nucleoli. In species with a single nucleolar bivalent, just one nucleolus is formed, while in those with multiple nucleolar bivalents a variable number of nucleoli are formed by association of different nucleolar bivalents or NORs that occupy the same nuclear peripheral space (Phyllotis and man). It can be concluded that the position of each nucleolus within the spermatocyte nucleus is mainly dependent upon: (1) the position of the NOR in the nucleolar bivalent synaptonemal complex (SC), (2) the nuclear pathway of the nucleolar bivalent SC, being both telomeric ends attached to the nuclear envelope, and (3) the association between nucleolar bivalents by means of their NOR-nucleolar domains that occupy the same nuclear space. Thus, the distribution of nucleoli within the nuclear space of spermatocytes is non-random and it is consistent with the existence of a species-specific meiotic nuclear architecture.

[Activation of nucleolar organizers during in vitro cultivation of mouse R1 embryonic stem cells]

We studies the activities of ribosomal genes (nucleolus forming regions of chromosomes) at successive stages of cultivation of the mouse R1 embryonic stem cells. The total number and number of active nucleolar organizers were estimated by means of in situ hybridization with mouse rDNA probes and argentophilic staining of nucleolus forming chromosomes regions from the 16th until the 32nd passages. The data we obtained suggest that the total number of nucleolar organizers per metaphase plate was constant (as a rule, eight), while the mean number of active nucleolar organizers progressively increased from the early (16th) to the late (32nd) passages: 5.2 +/- 0.4 versus 7.4 +/- 0.9 argentophilic organizers per cell. Cell heterogeneity by the number of active nucleolar organizers also increased during the late passages. Taken together, these data suggest activation of DNA transcription and synthesis of ribosomes during cultivation of mouse R1 embryonic stem cells. Based on the experimental and published data, it has been proposed that activation of ribosomal genes correlates in time with a decreased capacity of embryonic stem cells for pluripotent differentiation.

Effects of vitrification in open pulled straws on the cytology of in vitro matured prepubertal and adult bovine oocytes

This study was designed to evaluate the effects of the cryopreservation of oocytes obtained from prepubertal calves or adult cows on chromosome organization, spindle morphology, cytoskeleton structures, and the ability of fertilized oocytes to develop to the blastocyst stage. Once in vitro matured (IVM), the oocytes were divided into three groups according to whether they were: (1) left untreated (control); (2) exposed to cryoprotectant agents (CPAs); or (3) cryopreserved by the open-pulled-straw (OPS) vitrification method. After thawing, oocyte samples were fixed, stained using specific fluorescent probes and examined under a confocal microscope. The remaining oocytes were fertilized, and cleavage and blastocyst rates recorded. After vitrification or CPA exposure, significantly higher proportions of oocytes showed changes in spindle morphology compared to the control group. The spindle structure of the adult cow IVM oocytes was significantly more resistant to the OPS vitrification process. Vitrification of oocytes from calves or adult cows led to significantly increased proportions of oocytes showing discontinuous or null actin staining of the cytoskeleton compared to non-treated controls. Oocytes only exposed to the cryoprotectants showed a similar appearance to controls. A normal distribution of actin microfilaments was observed in both calf and adult cow oocytes, irrespective of the treatment. Cleavage and blastocyst rates were significantly lower for vitrified versus non-treated oocytes. Oocytes obtained from adult cows were more sensitive to CPA exposure, while the vitrification procedure seemed to have more detrimental effects on the calf oocytes.

[Localization of chromosomal nucleus organizing regions in one-cell mouse embryos and oocytes by fluorescence in situ hybridization]

In mouse zygotes, ribosomal genes (rDNA) are transcriptionally silent and so-called "nucleolar precursor bodies" are present instead of typical nucleoli. However, the functional significance of these structures remains obscure. Specifically, it remains unknown whether structural association between the nucleolar precursor bodies and rDNA are maintained when rDNA synthesis is switched off. Here, we studied for the first time the rDNA topology in one-cell mouse embryos and MII oocytes using fluorescence in situ hybridization and mouse rDNA probes. Our data suggest that in the pronuclei of one-cell embryos, rDNAs form rather compact clusters, whose number does not exceed that of nucleolus organizing chromosomes characteristic for the haploid set of mouse chromosomes. In zygotic pronuclei, not all nucleolar precursor bodies are associated with rDNA and not all rDNA repeats are attached to the nucleolar precursor bodies. Altogether, these data favor the idea that spatial interactions of nucleolus organizing chromosomes and nucleolar precursor bodies are not obligatory. We assume that associations between nucleolar precursor bodies and nucleolus organizing chromosomal regions are mediated by centromeric heterochromatin. The total numbers of silver stained nucleolus organizing chromosomes in CBA and C57BL mice are different. rDNA genes are unequally distributed among nucleolus organizing chromosomes and nucleolus organizing regions of sister chromatids.

Multicolor spectral karyotyping of rat chromosomes

Rat and mouse have become important animal models to study various human diseases such as cancer. Cytogenetic analysis of the respective karyotypes is frequently required to investigate the causative genetic defects and especially neoplastic cells often show complex chromosome aberrations and many different marker chromosomes. However, structural homogeneity of the chromosomes in these species as well as less pronounced differences in banding patterns make it difficult to assign genetic abnormalities to certain chromosomes by conventional banding techniques. Here we report for the first time the successful application of multicolor spectral karyotyping (SKY) to rat chromosomes, which allows unequivocal identification of all rat chromosomes with the exception of chromosomes 13 and 14 in different colors, thus enabling the elucidation of even complex rearrangements in the rat karyotype. Flow-sorted chromosome specific painting probes for all 22 rat chromosomes (20 autosomes, X, and Y) were combinatorially labeled by a set of five different fluorochromes and hybridized in situ to metaphase spreads of a healthy rat, to diakineses from testicular material, and to cells from a rat FAO hepatoma cell line. Measuring the complete spectrum at each image point by using the SpectraCube((R)) spectral imaging system and respective computer software allowed identification of the individual rat chromosomes by their specific emission spectra. Classification algorithms in the analysis software can then display the rat chromosomes in specific pseudo-colors and automatically order them in a karyotype table. After its successful application to human and mouse chromosomes, spectral karyotyping of rat chromosomes now also allows cytogenetic screening of the complete rat genome by a single hybridization.

Morphological, chromosomal, and molecular evolution are uncoupled in pocket mice

C-, and G-banded chromosomes are presented for Perognathus amplus and Perognathus longimembris from Arizona, USA and Chaetodipus nelsoni from Coahuila, Mexico. The two species of Perognathus reveal similar C-band patterns, and extensive autosomal and X chromosome G-band identity with only pericentric inversions distinguishing pairs 4 and 6 and a difference in the morphology of pair 20. Three pairs of autosomal secondary constrictions were found in P. amplus and only one in P. longimembris. Only 50% of the amplus/longimembris G-banded karyotype could be aligned with that of C. nelsoni indicating extensive chromosomal restructuring has taken place since these genera last shared a common ancestor. A review of the literature suggests variable rates of morphological, chromosomal and molecular evolution in these animals.

Knockout mice provide novel insights into meiotic chromosome and telomere dynamics

Meiosis is a succession of two specialized cell divisions that leads to the formation of gametes and thereby compensates for genome doubling at fertilization. During the extended prophase of the first meiotic division chromosomes assemble protein cores (axial elements) that attach their ends to the nuclear envelope. These ends transiently gather at a limited sector of the nuclear periphery (bouquet stage) at a time when meiotic recombination is initiated and when chromosomes initiate stable pairing (synapsis). This review discusses novel insights into the relation between recombinational DNA repair and meiotic telomere dynamics that have arrived from recent studies of transchromosomal mice and knockout mice. Analysis of mice deficient for A-type lamins, histone H2AX, Suv39h HMTases, and the AE protein SYCP3 suggests that entry into prophase I requires heterochromatin integrity and lamin A expression. Initiation of meiotic telomere clustering represents an early recombination-independent event in first meiotic prophase, while exit from the bouquet stage depends on signals that emanate from the progress of recombinational DNA repair as sensed by ATM kinase and relayed through histone H2AX.

Cytogenetic mapping and orientation of the rhesus macaque MHC

Applying fluorescence in situ hybridisation (FISH), six cosmid clones of rhesus macaque origin containing the genes SACM2L, RING1, BAT1 and MIC2, MIC3, MICD, and MOG of the major histocompatibility complex (MHC) were localised to the long arm of the rhesus macaque chromosome 6 in 6q24, the orthologous region to human 6p21.3. Furthermore, centromere to telomere orientation of the rhesus macaque MHC as well as the internal order of the MHC genes tested are the same as in human. Fiber-FISH allows a rough estimate of distances between these MHC genes in the rhesus macaque, and, as in the human, the rhesus macaque MHC comprises about 3 to 4 Mb.

The Centrosome in Higher Organisms: Structure, Composition, and Duplication

The centrosome found in higher organisms is an organelle with a complex and dynamic architecture and composition. This organelle not only functions as a microtubule-organizing center, but also is integrated with or impacts a number of cellular processes. Defects associated with this organelle have been linked to a variety of human diseases including several forms of cancer. Here we review the emerging picture of how the structure, composition, duplication, and function of the centrosome found in higher organisms are interrelated.

Isolation of chromosomal regions controlling intersex development in a marsupial

A marsupial (Sminthopsis douglasi) with bilateral intersexuality had a hemiscrotum on the right side and a hemi-pouch with nipples on the left. A normal female karyotype (2n = 14, XX) was present in cells from the right (male) side, while cells from the left (female) side initially had a female karyotype plus two dot-like chromosomes (2n = 14, XX + 2B). It is proposed that the dots represented a region deleted from the X chromosome that contains the "pouch-mammary/scrotum" (PMS) switch gene whose dosage determines development of a pouch and teats (two doses) or a scrotum (one dose). Mis-segregation early in embryonic development produced a lineage with one normal X and one deleted X (male side), and a lineage with a normal and deleted X, plus two copies of the deleted region (female side). The origin of the supernumerary elements was therefore investigated in the expectation that they may contain the long-sought pouch-mammary/scrotum switch gene. Several elements were microdissected, and amplified DNA was used for in situ hybridization, producing signals in five different chromosome regions including the X. This could represent a region of the X that contains, as well as PMS, repetitive DNA that is present also at other chromosomal sites.

A new FISH assay to simultaneously detect structural and numerical chromosomal abnormalities in mouse sperm

De novo aberrations in chromosome structure represent important categories of paternally transmitted genetic damage. Unlike numerical abnormalities, the majority of de novo structural aberrations among human offspring are of paternal origin. We report the development of a three-color fluorescence in situ hybridization (FISH) assay (CT8) to detect mouse sperm carrying structural and numerical chromosomal abnormalities. The CT8 assay uses DNA probes for the centromeric and telomeric regions of chromosome 2, and a probe for the subcentromeric region of chromosome 8. The CT8 assay was used to measure the frequencies of sperm carrying certain structural aberrations involving chromosome 2 (del2ter, dup2ter, del2cen, dup2cen), disomy 2, disomy 8, and sperm diploidy. Analysis of approximately 80,000 sperm from eight B6C3F1 mice revealed an average baseline frequency of 2.5 per 10,000 sperm carrying partial duplications and deletions of chromosome 2. Extrapolated to the entire haploid genome, approximately 0.4% of mouse sperm are estimated to carry structural chromosomal aberrations, which is more than fivefold lower than the spontaneous frequencies of sperm with chromosome structural aberrations in man. We validated the CT8 assay by comparing the frequencies of abnormal segregants in sperm of T(2;14) translocation carriers detected by this assay against those detected by chromosome painting cytogenetic analysis of meiosis II spermatocytes. The CT8 sperm FISH assay is a promising method for detecting structural chromosome aberrations in mouse sperm with widespread applications in genetics, physiology, and genetic toxicology.

[Application of atomic force microscopy in the study of morphology of double minute chromosomes]

Atomic force microscopy (AFM) has many advantages in the study of biological samples, such as the convenient specimen preparation and the high resolution. In the present study, AFM was used to observe the double minute chromosomes (DMs) in mouse methotrexate-resistant cell line 3T3R500. AFM images were obtained by tapping mode, contact mode and later force mode of AFM. DMs were composed of two compact spheres connected with fibers. The number of DMs in the 3T3R500 cells increased with increasing levels of methotrexate (MTX) resistance. The data of the height and the underside diameter of the DMs were also obtained. The details of specimen preparation and scan mode selection of AFM were discussed. Our results show that AFM is a powerful method in the study of DMs.

Establishment of an R-banded rabbit karyotype nomenclature by FISH localization of 23 chromosome-specific genes on both G- and R-banded chromosomes

Direct detection of fluorescent in situ hybridization signals on R-banded chromosomes stained with propidium iodide is a rapid and efficient method for constructing cytogenetic maps for species with R-banded standard karyotypes. In this paper, our aim is to establish an R-banded rabbit karyotype nomenclature that is in total agreement with the 1981 G-banded standard nomenclature. For this purpose, we have produced new GTG- and RBG-banded mid-metaphase karyotypes and an updated version of ideograms of R-banded rabbit chromosomes. In addition, to confirm correlations between G- and R-banded chromosomes, we have defined a set of 23 rabbit BAC clones, each containing a specific gene, one marker gene per rabbit chromosome, and we have localized precisely each BAC clone by FISH on both G- and R-banded chromosomes.

Chromosome rearrangements between chicken and guinea fowl defined by comparative chromosome painting and FISH mapping of DNA clones

Chromosome homology between chicken (Gallus gallus) and guinea fowl (Numida meleagris) was investigated by comparative chromosome painting with chicken whole chromosome paints for chromosomes 1-9 and Z and by comparative mapping of 38 macrochromosome-specific (chromosomes 1-8 and Z) and 30 microchromosome-specific chicken cosmid DNA clones. The comparative chromosome analysis revealed that the homology of macrochromosomes is highly conserved between the two species except for two inter-chromosomal rearrangements. Guinea fowl chromosome 4 represented the centric fusion of chicken chromosome 9 with the q arm of chicken chromosome 4. Guinea fowl chromosome 5 resulted from the fusion of chicken chromosomes 6 and 7. A pericentric inversion was found in guinea fowl chromosome 7, which corresponded to chicken chromosome 8. All the chicken microchromosome-specific DNA clones were also localized to microchromosomes of guinea fowl except for several clones localized to the short arm of chromosome 4. These results suggest that the cytogenetic genome organization is highly conserved between chicken and guinea fowl.

Generation of chromosome paints: approach for increasing specificity and intensity of signals

Chromosome painting is a widely used technique, and the two principal means of generating probes for such experiments involve DNA isolation by chromosome flow sorting and by chromosome microdissection. Frequently, chromosome paints are bright and specific; however, on occasion, signals can be weak and nonspecific, particularly for microdissected probes. Reasons for this have been attributed to co-amplification of non-target DNA and the formation of primer concatamers during degenerate oligonucleotide primed (DOP)-PCR. Here we describe a technique of circumventing this problem by sequence enrichment. It involves co-hybridization of DOP-PCR biotinylated microdissected material and linkered genomic DNA. Biotinylated DNA fragments captured on streptavidin-coated paramagnetic beads are eluted and amplified by PCR using a single primer complementary to the linker arm.

Three-dimensional helical coiling structures and band patterns of hydrous metaphase chromosomes observed by low vacuum scanning electron microscopy

Helical coiling structures and band patterns of hydrous metaphase chromosomes were documented three-dimensionally by low vacuum scanning electron microscopy (SEM). Fixed or unfixed isolated Chinese hamster metaphase chromosomes were stained with platinum blue (Pt blue) and observed in the backscattered electron mode for low vacuum SEM without any hypotonic treatment or drying processes. Fibrous structures were shown both in the fixed and unfixed hydrous chromosomes; helical chromatid coils and their subcoils were clarified especially in the fixed chromosomes having contrasting alternative bands of light and darkness, while the translucent perichromosomal matrix and compact fibrous structures were recognized in the unfixed chromosomes. The helical coils were more clearly represented in a loosened chromatid of metaphase chromosomes. Treatment with a tris-HCl buffer solution and Pt blue staining in a hydrous condition successfully produced banding patterns similar to G-bands on metaphase chromosomes. These banded chromosomes observed by low vacuum SEM were also analyzed stereoscopically by field emission SEM after critical point drying. These findings indicate that: 1) native or unfixed chromosomes maintain the compact arrangement of high-order helical structures covered with the peri-chromosomal matrix; 2) helical coiling appearances of chromatids frequently observed in previous papers might be caused by loosening of the final level of the high-order structure of the metaphase chromosome; and 3) banding patterns might be produced by the rearrangement or reorganization of chromatin fibers at the 30 nm fiber level after the extraction of some chromosomal components including the peri- or intra-chromosomal materials during the banding procedure.