Chromosomes and their relationship to nuclear components during the cell cycle in Chinese hamster cells

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.

Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins

To study the possible role of the nuclear matrix in chromosome territory organization, normal human fibroblast cells are treated in situ via classic isolation procedures for nuclear matrix in the absence of nuclease (e.g., DNase I) digestion, followed by chromosome painting. We report for the first time that chromosome territories are maintained intact on the nuclear matrix. In contrast, complete extraction of the internal nuclear matrix components with RNase treatment followed by 2 M NaCl results in the disruption of higher order chromosome territory architecture. Correlative with territorial disruption is the formation of a faint DNA halo surrounding the nuclear lamina and a dispersive effect on the characteristically discrete DNA replication sites in the nuclear interior. Identical results were obtained using eight different human chromosome paints. Based on these findings, we developed a fractionation strategy to release the bulk of nuclear matrix proteins under conditions where the chromosome territories are maintained intact. A second treatment results in disruption of the chromosome territories in conjunction with the release of a small subset of acidic proteins. These proteins are distinct from the major nuclear matrix proteins and may be involved in mediating chromosome territory organization.

Spatial and temporal dynamics of DNA replication sites in mammalian cells

Fluorescence microscopic analysis of newly replicated DNA has revealed discrete granular sites of replication (RS). The average size and number of replication sites from early to mid S-phase suggest that each RS contains numerous replicons clustered together. We are using fluorescence laser scanning confocal microscopy in conjunction with multidimensional image analysis to gain more precise information about RS and their spatial-temporal dynamics. Using a newly improved imaging segmentation program, we report an average of approximately 1,100 RS after a 5-min pulse labeling of 3T3 mouse fibroblast cells in early S-phase. Pulse-chase-pulse double labeling experiments reveal that RS take approximately 45 min to complete replication. Appropriate calculations suggest that each RS contains an average of 1 mbp of DNA or approximately 6 average-sized replicons. Double pulse-double chase experiments demonstrate that the DNA sequences replicated at individual RS are precisely maintained temporally and spatially as the cell progresses through the cell cycle and into subsequent generations. By labeling replicated DNA at the G1/S borders for two consecutive cell generations, we show that the DNA synthesized at early S-phase is replicated at the same time and sites in the next round of replication.

Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin

A number of structural and functional subnuclear compartments have been described, including regions exclusive of chromosomes previously hypothesized to form a reactive nuclear space. We have now explored this accessible nuclear space and interchromosomal nucleoplasmic domains experimentally using Xenopus vimentin engineered to contain a nuclear localization signal (NLS-vimentin). In stably transfected human cells incubated at 37 degrees C, the NLS-vimentin formed a restricted number of intranuclear speckles. At 28 degrees C, the optimal temperature for assembly of the amphibian protein, NLS-vimentin progressively extended with time out from the speckles into strictly orientated intranuclear filamentous arrays. This enabled us to observe the development of a system of interconnecting channel-like areas. Quantitative analysis based on 3-D imaging microscopy revealed that these arrays were localized almost exclusively outside of chromosome territories. During mitosis the filaments disassembled and dispersed throughout the cytoplasm, while in anaphase-telophase the vimentin was recruited back into the nucleus and reassembled into filaments at the chromosome surfaces, in distributions virtually identical to those observed in the previous interphase. The filaments also colocalized with specific nuclear RNAs, coiled bodies and PML bodies, all situated outside of chromosome territories, thereby interlinking these structures. This strongly implies that these nuclear entities coexist in the same interconnected nuclear compartment. The assembling NLS-vimentin is restricted to and can be used to delineate, at least in part, the formerly proposed reticular interchromosomal domain compartment (ICD). The properties of NLS-vimentin make it an excellent tool for performing structural and functional studies on this compartment.

Nuclear architecture and the induction of chromosomal aberrations

Progress in fluorescence in situ hybridization, three dimensional microscopy and image analysis has provided the means to study the three-dimensional structure and distribution of chromosome territories within the cell nucleus. In this contribution, we summarize the present state of knowledge of the territorial organization of interphase chromosomes and their topological relationships with other macromolecular domains in the human cell nucleus, and present data from computer simulations of chromosome territory distributions. On this basis, we discuss models of chromosome territory and nuclear architecture and topological consequences for the formation of chromosome exchanges.

Chromosome topology in mammalian interphase nuclei

Since 1968, when Comings published the pioneering paper on "the rationale for an ordered arrangement of chromatin in the interphase nucleus," technical methods have progressed tremendously and improved our understanding of interphase organization. The existence of highly ordered organizational patterns of the cell nucleus appears to be beyond any doubt and it is difficult to escape the conclusion that interphase chromosome topology is important for the complex regulation of the many varied and interrelated nuclear processes. However, it is worth emphasizing that a universally valid principle of chromosome arrangement does not exist and, therefore, any generalization of interphase patterns can be misleading. The factors of order according to which the chromosomes are arranged inside the nucleus are manifold: (1) Individual chromosomes remain in spatially separated domains throughout interphase, preventing an intermingling of the decondensed euchromatin. (2) Chromosome regions that contain constitutive heterochromatin associate into larger chromocenters. (3) In most cell types direct associations between interphase domains of homologous chromosomes are not observed. In others homologous heterochromatic regions tend to be paired preferentially. (4) Interphase chromosomes do not float freely in the nucleoplasm; they are associated to varying degrees with the nuclear membrane and other components of the nuclear scaffold. The number of attachment sites for each chromosome to the nuclear membrane is relatively low. (5) The positions of centromeres (and pericentromeric heterochromatin) are nonrandom and characteristic of each cell type. Specific centromere movements occur during the cell cycle, during differentiation, and under certain pathophysiological conditions. (6) The telomeric chromosome ends are particularly prone to associate in certain somatic cell types and in meiotic prophase cells. (7) The arrangement of repetitive DNA families appears to determine a structural framework of the interphase nucleus. Different cell types of one organism can exhibit marked differences in their repetitive DNA framework, whereas cells that are in an identical differentiated state or an identical phase of the cell cycle often show comparable interphase patterns even in evolutionarily distant species. (8) The various steps of ribosome biogenesis take place in a precise fashion within a separate nuclear domain, the nucleolus. The topologically well-defined nucleolar substructures are required for rDNA transcription and pre-rRNA processing. (9) A compartmentalization of transcriptional and processing events is also evident in the rest of the nucleus. However, it is not yet known if the in situ sites of transcription and RNA processing for a particular (nonribosomal) gene or gene family are actually adjacent. (10) DNA replication is precisely spatiotemporally regulated within the nucleus. The replication domains are immobilized on the nuclear matrix.(ABSTRACT TRUNCATED AT 400 WORDS)