The quinternary chromatin-DNA structure. Three-dimensional reconstruction and functional significance

High order DNA structure as inferred by optical fluorimetry and scanning calorimetry

New quantitative insights on the native high order chromatin-DNA structure existing within interphase nuclei are obtained by monitoring the effects of two common well-characterized fixatives, glutaraldehyde and ethanol/acetic acid mixture, at the level of the intranuclear DNA distribution and structures. Reproducible distinct levels of DNA fluorescence intensity and their intranuclear distribution are apparent in unfixed and fixed thymocytes by using DAPI and quantitative optical microscopy based on a charge coupled device. The fluorescent histograms correlated with the calorimetric thermograms on the very same thymocytes fixed and unfixed, establish an unequivocal baseline for the different levels of structural organization of the chromatin within the intact nucleus; namely their number, DNA packing ratio and fiber diameter. A systematic comparison among all the numerous models, being so far proposed for the quinternary and quaternary levels of DNA folding, to identifies the rope or ribbon-like and the chromonema as the ones that best fit with the in situ distribution.

Fluorescence cytometry of microtubules and nuclear DNA during cell-cycle and reverse-transformation

Synchronized CHO-K1 cells and their dibutyryl c-AMP treated counterparts have been characterized by means of static and flow fluorescence cytometry at the level of nuclear DNA and cytoplasmic microtubules. In order to confirm earlier findings on synchronized population, Carnoy fixed and hydrolyzed, several new findings are here reported at the level of single intact cell. The fluorescence intensity of DAPI-stained glutaraldehyde fixed 2C cells correlates well with the average absorbance of the corresponding Feulgen-stained cells, thereby appearing also to be a measure of chromatin condensation during the G1 phase. In the early part of G1, the drastic alteration in anti-beta tubulin immunostaining is shown to parallel microtubule depolymerization induced by calcium or colcemide. The known 1-2 h lengthening of the G1 period after reverse-transformation appears to correlate with a similar delay in the abrupt chromatin decondensation. The above results are discussed in terms of the role of microtubules and nuclear morphometry (and their coupling) in the control of cell cycle progression of transformed vs. fibroblast-like cells.

Nuclear structure and the three-dimensional organization of DNA

The organization of DNA within the nucleus has been demonstrated to be both cell and tissue specific and is arranged in a non-random fashion in both sperm and somatic cells. Nuclear structure has a pivotal role in this three-dimensional organization of DNA and RNA and contributes as well to forming fixed organizing sites for nuclear functions, such as DNA replication, transcription, and RNA processing. In sperm, DNA is also organized in a specific fashion by the nuclear matrix and DNA-protamine interactions. Within somatic cells, the nuclear matrix provides a three-dimensional framework for the tissue specific regulation of genes by directed interaction with transcriptional activators. This differential organization of the DNA by the nuclear matrix, in a tissue specific manner, contributes to tissue specific gene expression. The nuclear matrix is the first link from the DNA to the entire tissue matrix system and provides a direct structural linkage to the cytomatrix and extracellular matrix. In summary, the tissue matrix serves as a dynamic structural framework for the cell which interacts to organize and process spatial and temporal information to coordinate cellular functions and gene expression. The tissue matrix provides a structural system for integrating form and function.

Chromatin texture changes related to proliferation and maturation in erythrocytes

Erythroid cell types were quantitatively assessed on the basis of the analysis of their nuclear images after Feulgen and Heidenhain blue counterstaining. An original nonsupervised classification method, developed in our laboratory, was applied to cell cycle analysis. Results obtained suggest that, in the four proliferative generation cycles, which concur with the successive morphological stages, there is a sequential flow of cells from one morphological stage to the next by cell cycling. We show that the chromatin pattern alone made it possible to set up a metric of the whole differentiation process occurring in the normal human erythroblastic lineage in which proliferating events occur.

Symmetry analysis of cell nuclei

An algorithm is described that is used to analyze the two-dimensional spatial symmetry of cell nuclei. The method provides two symmetry features: the symmetry index (SI), which estimates the precise spatial symmetry of a given chromatin component, Cn, and the quadrant symmetry index (QSI), which estimates the number of quadrants being occupied by Cn. A previous analysis is used to show that age-related change in Malpighian tubule nuclei from the adult housefly is associated with significant alterations in the spatial symmetry of low-, medium-, and high-density chromatin components (LDC, MDC, HDC). This included a seven-fold increase in the spatial symmetry of HDC and a shift in the symmetry profile (from highest to lowest degree of symmetry) from LDC-MDC-HDC to MDC-LDC-HDC. The increased spatial symmetry of HDC suggests that it occurs at new nuclear sites as the fly ages and that these sites are distributed over approximately 60% of the chromosome population.

The relative intranuclear positions of Barr bodies in XXX non-transformed human fibroblasts

The extent to which chromosomes exist in an ordered three-dimensional arrangement within the interphase nucleus remains unknown. As a means of tackling this issue we have developed simple statistical methods to test whether the positions of any intranuclear markers are mutually correlated. Applying these methods to non-transformed XXX human fibroblasts as a test case, we have examined the relative nuclear locations of the two Barr bodies in 2C cells of this type. Our results show that while individual Barr bodies have a highly non-random intranuclear distribution, segregating preferentially at the nuclear periphery in a plane parallel to the plane of cell growth (i.e., the substrate surface) and bisecting the nucleus, no evidence was found of any significant correlation between the positions of the two Barr bodies within a given nucleus.

Critical nuclear DNA size and distribution associated with S phase initiation. Peripheral location of initiation and termination sites

Using HeLa S-3 cells synchronized by selective detachment, in this paper we report a parallel study of nuclear morphology and autoradiography grain patterns between middle G1 and middle S phases. Our results show two distinct [3H]-thymidine labeling patterns. The first "peripheral" labeling pattern has a characteristic nuclear size distribution, in contrast to the heterogeneous and varying size distributions of Feulgen-stained nuclei, and apparently is characteristic of very early S phase. The sizes of the second labeling pattern--homogeneous or inhomogeneous grain distribution throughout the nucleus--are equal or larger than the first and vary with S phase progression. Together, the corresponding nuclear sizes of the labeled nuclei represent the larger extreme of nuclear areas, and the labeling index closely parallels the fraction of nuclei with areas larger than the minimum size of the labeled nuclei. These results suggest a characteristic nuclear size (reflecting unique intranuclear DNA distribution) as a necessary, if not sufficient, requirement for S phase initiation. Parallel experimentation with rat liver cells-synchronized in vivo by partial hepatectomy and analyzed by thin section autoradiography--confirms the existence of a peripheral labeling pattern in both the very early part and the very late part of S phase, which reconciles our data with previous results and points to the fact that both initiation and termination sites for DNA replication are near the nuclear periphery.

Three-dimensional chromatin distribution in neuroblastoma nuclei shown by confocal scanning laser microscopy

The relationship between cell shape and function has long been of interest. However, although the behaviour of the cytoskeleton during the cell cycle has been studied extensively variations in the shape and three-dimensional substructure of the nucleus are less well documented. The spatial distribution of chromatin has previously been studied by a mathematical analysis of the optical densities of stained nuclei, allowing an indirect derivation of the three-dimensional distribution of chromatin. More direct information on chromatin organization can be obtained from electron-microscopic serial sections, although this is very laborious. Using an iterative deconvolution algorithm, Agard and Sedat achieved a degree of optical sectioning in conventional fluorescence microscopy and reconstructed the three-dimensional arrangement of polytene chromosomes. We report here on the three-dimensional structure of cultured mammalian cells as visualized by confocal scanning laser microscopy (CSLM). The exceptionally short depth of field of this imaging technique provides direct optical sectioning which, together with its higher resolution, makes CSLM extremely useful for studying the three-dimensional morphology of biological structures.

The G1 period. Two cycles of chromatin conformational changes monitored by single cell dye intercalation

In previous papers the existence of two cycles of chromosome condensation-decondensation per cell cycle was suggested based on experiments involving nuclear morphometry measurements of Feulgen-stained nuclei. This conclusion can be criticized since its assumption of a relationship between nuclear morphology and chromatin structure is derived from indirect evidence. In this paper, we report simultaneous measurements of nuclear area and nuclear fluorescence intensity on individual cells stained with the intercalating dye, acridine orange (AO). Using cells in various stages of G1 and synchronized by two different methods, our results demonstrate a linear correlation between nuclear area and fluorescence intensity. They also indicate two cycles of chromatin condensation-decondensation during the G1 period, as assayed by the number of chromatin primary, intercalating AO binding sites. Finally, they show that the first of these cycles involves a transition in early G1 from a very small condensed nucleus (immediately after telephase) to a relatively large, dispersed nucleus that occurs abruptly.

Normal versus abnormal cell proliferation. A unitary and analytical overview

The most recent findings on the molecular and cellular characterization of normal and abnormal cell proliferation are summarized. They include molecular spectroscopy, nucleic acid conformation, protein modifications, premature chromosome condensation, nucleoli changes, nuclear and cell morphometry, image analysis, flow microfluorimetry, and time-lapse cinematography. Biophysical and biochemical evidence in favor or against two cycles of chromatin condensation, followed by two abrupt random decondensations, per cell cycle are presented. Other biphasic changes at the molecular and cellular levels that favor the existence of two random transitions, or restriction points, per cell cycle are discussed. A comprehensive unitary model of the cell cycle is then outlined; this model is able to explain most findings on continuously dividing cells and on quiescent cells induced to proliferate. Within this analytical framework the physical-chemical and biological properties are given, in either normal or tumor cells, for the various types of "noncycling" cells that are here viewed as necessary steps in mammalian cell growth rather than separates states. The implications of the coupling of higher-order chromatin structure with cell geometry and growth, high in fibroblast-like cells but low in transformed cells, are also discussed. Molecular mechanisms likely responsible for the chromatin conformational changes occurring at the G0 leads to G1, G1 leads to S, G2 leads to M transitions are finally discussed in terms of polyelectrolyte theory.