Structural organization of chromosomes in interphase nuclei

Nuclear remodeling in response to steroid hormone action

Steroid and similar hormones comprise the broadest class of gene regulatory agents known, spanning vertebrates through the lower animals, and even fungi. Not unexpectedly, therefore, steroid receptors belong to an evolutionarily highly conserved family of proteins. After complexing with their cognate ligands, receptors interact with hormone response elements on target genes and modulate transcription. These actions are multifaceted and only partly understood, and include large-scale changes in the structure and molecular composition of the affected cell nuclei. This chapter examines steroid hormone action and the resultant nuclear remodeling from the following perspectives: (1) Where are the receptors located? (2) Which nuclear domains are most affected? (3) Are there extended or permanent nuclear changes? (4) What is the role of coiled bodies and similar structures in this regard? To address these and related questions, information is drawn from several sources, including vertebrates, insects, and malignant tissues. Entirely new data are presented as well as a review of the literature.

Effects of anisosmotic conditions on the cytoskeletal architecture of cultured PC12 cells

PC12 cells show a classical volume regulatory process when submitted to hypo-osmotic conditions. The present study examined the effects of such osmotic shock on the structural organization of different cytoskeletal elements. Results were obtained by use of different light and electron microscopy techniques combined with immunostaining methods. It appeared that the osmotically induced changes in cell volume were concomitant with important modifications in the organization of the microfilament network. Microfilaments concentrated in the perinuclear area, leaving only radial extensions of poorly organized structures in the cytoplasm. The latter were the only actin structures immunologically stained in the cytoplasm and seemed to anchor to the plasma membrane. Measurements of the fluorescence intensity of PC12 cells treated with FITC-labeled phalloidin indicated a progressive depolymerization, followed by a repolymerization of F-actin. This occurs in parallel with microfilament reorganization and volume regulatory processes. The appearance of microfilament reorganization was a function of both the incubation period and the amplitude of the osmolarity changes. During the first minutes of osmotic shock, a decrease was observed in the density and length of microvilli, which normally cover the PC12 cell surfaces, suggesting an early reorganization of the underlying microfilament network. Microtubules and intermediate filament networks were not affected by the hypo-osmotic conditions.

Interphase nuclear envelope lamins form a discontinuous network that interacts with only a fraction of the chromatin in the nuclear periphery

Antibodies directed against nuclear envelope lamin proteins have been used in conjunction with three-dimensional light and electron microscope methodologies to determine the spatial organization of lamins in diploid interphase nuclei and to relate this organization to the positions of chromatin in the nuclear periphery. Using Drosophila early embryos, Drosophila Kc cells, and human HeLa cells, it is qualitatively and quantitatively observed that lamins are organized as a highly discontinuous, apparently fibrillar network that leaves large voids in the nuclear periphery containing little or no lamin. Using fluorescence microscopy to compare and quantitate the relationship between chromatin and the lamin network, it is found that although there is a strong tendency for the most peripheral chromatin to be positioned directly underneath a lamin fiber, only a small fraction of the chromatin in the nuclear periphery is sufficiently close to a lamin fiber to possibly be in direct contact.

Ultrastructure of somatic and meiotic nucleoids

In this review emphasis is placed on the contribution of transmission electron microscopy to the analysis of spread chromosomes and nucleoids. Support is advanced for the DNA loop and rosette organization of meiotic and metaphase chromosomes and nucleoids. Extensive discussion is given to the biochemical treatments used for producing nucleoids and the effect of divalent cations and chelating agents on chromatin compactization (supercoiling). Detailed studies on nucleoids from hepatocytes are presented, with emphasis on the significance of DNA attachment to the internal nuclear matrix and to the nuclear lamina. It is firmly predicted that from the increasing knowledge of the structural organization of eukaryotic chromatin and the genome, a greater understanding of the functional roles of the various intranuclear structures will ultimately follow.

Localization of DNAase I-sensitive sequences to specific regions of interphase nuclei

Active or potentially active gene loci are preferentially sensitive to DNAase I digestion. Cedar and colleagues used this DNAase I sensitivity to label active sequences preferentially by nick translation of nuclei and chromosomes. Using biotinylated nucleotides and immunofluorescence detection, we have looked for compartmentalization of DNAase I-sensitive sequences by nick translation of nuclei maintained as three-dimensional structures. Labeled sequences in mouse L cells are preferentially localized at the nuclear periphery in both permeabilized nuclei and frozen sections. In newt and chicken nucleated erythrocytes, labeled regions are at borders of condensed chromatin masses along interchromatin channels communicating with the nuclear periphery. Control experiments indicate that nick translation of nuclei preferentially labels highly expressed genes and that the preferential localization of DNAase-I sensitive regions is probably not a consequence of fixation artifacts or selective nuclear permeability to the labeling reagents.

Effects of osmotic shocks on the ultrastructure of different tissues and cell types

This study deals with the effects of hyper- and hypo-osmotic media on the ultrastructure of four different types of cells and tissues: rat pheochromocytoma cells of line PC12, mouse Ehrlich ascites tumor cells, rat kidney cortex and intestine. Application of hyper-osmotic conditions induces in the nuclear compartment of the tested cell types a condensation of chromatin, a ruffling of the nuclear envelope with loosening of condensed chromatin from the lamina, and an apparent loss of nucleolar fibrillar component which disappears in a background of diffuse granular material. In hypo-osmotic media, there is a marked decondensation of chromatin and a fragmentation of the granular material of the nucleolus. As far as the cytoplasmic compartment is concerned, the electron density of the cytosol is markedly increasing when going from hypo- to hyper-osmotic conditions and there is no vacuolization in hypo-osmotic media. In kidney cortex slices, application of hypo-osmotic shocks further results in a marked reduction of the extracellular space delimited by the infoldings of the tubular cells plasma membranes. These modifications are discussed in relation to the volume regulation process and the changes in ion concentration that occur in cells submitted to anisosmotic media.

Variations in ADP-ribosylation of nuclear scaffold proteins during the HeLa cell cycle

Cell cycle variations in ADP-ribosylation of nuclear scaffold proteins were determined. Nuclei of synchronized cells were isolated and labeled with [32P]NAD before nuclear scaffolds were obtained by digestion of DNA with DNase I and extraction of proteins with 2M NaCl. Autoradiograms revealed the three groups of "lamins" and a species identified as poly (ADP-ribose) polymerase to be the primary ADP-ribosylated proteins. The patterns of modification of nuclear scaffold proteins displayed similar features through the cell cycle. Radioactivity in the lamins increased from 20% in early-S phase to 40% in G1 phase of the next cell cycle.

Changes in distribution of nuclear matrix antigens during the mitotic cell cycle

We examined the distribution of nonlamin nuclear matrix antigens during the mitotic cell cycle in mouse 3T3 fibroblasts. Four monoclonal antibodies produced against isolated nuclear matrices were used to characterize antigens by the immunoblotting of isolated nuclear matrix preparations, and were used to localize the antigens by indirect immunofluorescence. For comparison, lamins and histones were localized using human autoimmune antibodies. At interphase, the monoclonal antibodies recognized non-nucleolar and nonheterochromatin nuclear components. Antibody P1 stained the nuclear periphery homogeneously, with some small invaginations toward the interior of the nucleus. Antibody I1 detected an antigen distributed as fine granules throughout the nuclear interior. Monoclonals PI1 and PI2 stained both the nuclear periphery and interior, with some characteristic differences. During mitosis, P1 and I1 were chromosome-associated, whereas PI1 and PI2 dispersed in the cytoplasm. Antibody P1 heavily stained the periphery of the chromosome mass, and we suggest that the antigen may play a role in maintaining interphase and mitotic chromosome order. With antibody I1, bright granules were distributed along the chromosomes and there was also some diffuse internal staining. The antigen to I1 may be involved in chromatin/chromosome higher-order organization throughout the cell cycle. Antibodies PI1 and PI2 were redistributed independently during prophase, and dispersed into the cytoplasm during prometaphase. Antibody PI2 also detected antigen associated with the spindle poles.

Characteristic folding pattern of polytene chromosomes in Drosophila salivary gland nuclei

A computer-based system for recording and analysing light microscope images, combined with classical cytogenetic analysis, has revealed the spatial organization of the giant chromosomes of Drosophila salivary gland cells. Each polytene chromosome arm folds up in a characteristic way, contacts the nuclear surface at specific sites and is topologically isolated from all other arms.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

Surface structure of isolated metaphase chromosomes

The relationship between the surface protuberances of mitotic chromosomes isolated from HeLa cells and the underlying fiber organization was investigated by scanning electron microscopy (SEM). Chromosomes were isolated in the presence of 5.0 mM Mg2+ by a method which avoids the use of organic solvents and extremes of pH. Chromosomes in 5.0 mM Mg2+ are highly condensed with a relatively smooth surface structure. In 1.5 mM Mg2+, a knobby surface substructure became apparent, with the protuberances having a mean diameter of 691 +/- 96 A. The diameter was 647 +/- 76 A at a magnesium concentration of 0.5 mM, but was only 349 +/- 52 A at a concentration of 0.15 mM. In 0.05 mM Mg2+, the mean diameter had decreased to 299 +/- 47 A and the chromosomes had expanded such that the underlying fibers had become a predominant feature of the micrographs. The knobby appearance of the chromosomes most likely reflects a radial arrangement of the fibers, which loop back at the peripheries of the chromosomes.

THE DISTRIBUTION OF CHROMATIN IN THE INTERPHASE NUCLEUS OF ZEBRINA PENDULA

An investigation of nuclear organization in interphase root tip cells of Zebrina pendula Schnizl. showed that: (1) 40% of the BSG (Barium hydroxide/saline/Giemsa) treated nuclei had nonrandomly distributed chromocenters and (2) BrdU-FPG (5′-bromodeoxyuridine-fluorescence plus Giemsa) treated nuclei showed discrete staining patterns when exposed to BrdU for time intervals of two or more cell cycles. These data were interpreted as further evidence for an ordered spatial arrangement of chromosomal regions in the interphase nucleus.

Dispersed and compact chromatin demonstrated with a new EM method: phosphotungstic acid hematoxylin block-staining

Glutaraldehyde/KMnO4 double fixation and phosphotungstic acid hematoxylin (PTAH) block-staining, before dehydration were found to reveal, with great detail and sharpness, the nuclear distribution of compact heterochromatin masses as electron-lucent patches. By contrast the areas of decondensed and dispersed chromatin acquired a high electron density due to the binding of the large PTAH molecule to basic groups in the loosened chromatin network. The method was tested on human blood leukocytes, on the thymus gland from immature rats, containing mitotic figures, and on mature avian erythrocytes. The results indicated that each cell type acquires a specific pattern of electron densities in the nucleus which depends upon the relative amounts of compact and dispersed chromatin present in that nucleus. Since the tissues are stained in-block immediately after fixation, artifacts of stain localization, due to alcohol dehydration, are avoided. Thus, PTAH block-staining "translates" the state of aggregation of the chromatin into characteristic and specific density patterns of the nuclei. This method may prove useful in differentiating active from inactive portions of the genome, at the ultrastructural level.

The organization, composition and matrix of hepatocyte nuclei exposed to alpha-amanitin

Alterations in the structure and molecular composition of avian hepatocyte nuclei were compared following administration in vivo of lethal and sub-lethal doses of alpha-amanitin. This toxin interferes with extranucleolar transcription by direct inhibition of RNA polymerase II activity. the resultant effects include: extensive condensation of chromatin, displacement of nucleoplasmic contents and fragmentation of nucleoli. Changes in nuclear morphology were quantitated by stereometry and related to variations in RNA and residual, non-histone proteins (NHP). Gross alterations in nuclear structure and depletion of RNA and NHP levels were of similar magnitude with both doses of amanitin. The effects were fully reversible, however, with a minimal dose but terminal with a lethal dose. DNA and histone protein levels remained unchanged at all stages. These results imply that the process of transciption may itself keep and/or maintain chromatin in a dispersed state, and that in the absence of transcription chromatin naturally condenses. Modification of nuclear proteins may be necessary only to maintain chromatin compacted permanently or for extended periods of time. A model of nuclear organization is proposed to incorporate these considerations and to identify the probable location of the nuclear matrix in situ.

Structure of interphase nuclei in relation to the cell cycle. Chromatin organization in mouse L cells temperature-sensitive for DNA replication

Mutant lines of mouse L cells, TS A1S9, and TS C1, show temperature-sensitive (TS) DNA synthesis and cell division when shifted from 34 degrees to 38.5 degrees C. With TS A1S9 the decline in DNA synthesis begins after 6-8 h at 38.5 degrees C and is most marked at about 24 h. Most cells in S, G2, or M at temperature upshift complete one mitosis and accumulate in the subsequent interphase at G1 or early S as a result of expression of a primary defect, failure of elongation of newly made small DNA fragments. Heat inactivation of TS C1 cells is more rapid; they fail to complete the interphase in progress at temperature upshift and accumulate at late S or G2. Inhibition of both cell types is reversible on return to 34 degrees C. Cell and nuclear growth continues during inhibition of replication. Expression of both TS mutations leads to a marked change in gross organization of chromatin as revealed by electron microscopy. Nuclei of wild-type cells at 34 degrees and 38.5 degrees C and mutant cells at 34 degrees C show a range of aggregation of condensed chromatin from small dispersed bodies to large discrete clumps, with the majority in an intermediate state. In TS cells at 38.5 degrees C, condensed chromatin bodies in the central nuclear region become disaggregated into small clumps dispersed through the nucleus. Morphometric estimation of volume of condensed chromatin indicates that this process is not due to complete decondensation of chromatin fibrils, but rather involves dispersal of large condensed chromatin bodies into finer aggregates and loosening of fibrils within the aggregates. The dispersed condition is reversed in nuclei which resume DNA synthesis when TS cells are downshifted from 38.5 degrees to 34 degrees C. The morphological observations are consistent with the hypothesis that condensed chromatin normally undergoes an ordered cycle of transient, localized disaggregation and reaggregation associated with replication. In temperature-inactivated mutants, normal progressive disaggregation presumably occurs, but subsequent lack of chromatin replication prevents reaggregation.

Selective effects of nonionic detergent and salt solutions in dissolving nuclear envelope protein.?20U

Protein has been selectively extracted from isolated chicken erythrocyte nuclear envelope by (1) dilute MgCl2/Triton X-100 followed by (2) concentrated MgCl2/Triton X-100 solutions. Certain proteins appear to be selectively dissolved in the first solvent and may occur in the nuclear envelope primarily as lipoproteins. Among the proteins insoluble in the low MgCl2/Triton X-100 wash, as well as in 500 mM MgCl2 without Triton previously used in the preparation of the envelope fraction, the quantitatively major polypeptides dissolve in a combination of high MgCl2 and Triton X-100. Further, much of this dissolved protein precipitates when the MgCl2 concentration is lowered by dialysis. The insolubility of these proteins appears to result from a combination of ionic and hydrophobic interactions and may explain the resistance of nuclei to various manipulative procedures including nonionic detergent washes. The procedures described provide a route for gently and selectively dissolving representative proteins from the nuclear envelope lipoprotein matrix and from the envelope "residual" protein.

Evolution of genome size by DNA doublings

Logarithmic distributions of nucleic acid contents per genome of species within major phylogenetic groups of organisms tend to form several peaks. These peaks appear to represent intragroup doublings of DNA or RNA which, in the case of eukaryotes, are independent of polyploidy. This phenomenon has been termed cryptopolyploidy. There are numerical similarities in peak values for different taxonomic groups. A high degree of order is suggested when minimum values for the major phylogenetic groups are plotted against a series of theoretical doublings. These data demonstrate the apparent existence of an exponential periodicity over eight orders of magnitude, leading us to suggest an evolutionary continuity of doublings of a basic ancestral genome (of about 300 nucleotides), these doublings being independent of both chromosome number and ploidy level. This proposed continuity encompasses most major life forms and is generally concomitant with increasing evolutionary complexity, particularly in the prokaryotes and lower eukaryotes. Our interpretation of the data presented here must currently be viewed as speculative, and we do not propose that genome doubling is the only mechanism for genome evolution. However, we feel that the evidence is sufficient to warrant serious scrutiny of our proposals. We hope that this approach to a synthesis of available data will provoke discussion and will stimulate further work toward either supporting, modifying, or disproving our hypothesis.

DNA denaturation in situ. Effect of divalent cations and alcohols

Heat denaturation profiles of rat thymus DNA, in intact cells, reveal the presence of two main DNA fractions differing in sensitivities to heat. The thermosensitive DNA fraction shows certain properties similar to those of free DNA: its stability to heat is decreased by alcohols and is increased in the presence of the divalent cations Ca2+, Mn2+, or Mg2+ at concentrations of 0.1-1.0 mM. Unlike free DNA, however, this fraction denatures over a wide range of temperature, and is heterogeneous, consisting of at least two subfractions with different melting points. The thermoresistant DNA fraction shows lowered stability to heat in the presence of Ca2+, Mn2+, or Mg2+ and increased stability in the presence of alcohols. It denatures within a relatively narrow range of temperature, consists of at least three subfractions, and, most likely, represents DNA masked by histones. The effect of Ca2+, Mn2+, or Mg2+ in lowering the melting point of the thermoresistant DNA fraction is seen at cation concentrations comparable to those required to maintain gross chromatin structure in cell nuclei or to support superhelical DNA conformation in isolated chromatin (0.5-1.0 mM). It is probable that factors involved in the maintenance of gross chromatin organization in situ and/or related to DNA superhelicity also have a role in modulating DNA-histone interactions, and that DNA-protein interactions as revealed by conventional methods using isolated chromatin may be different from those revealed when gross chromatin morphology remains intact.

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.

The ultrastructure of dyserythropoiesis in aplastic anaemia

Electron microscopy of erythropoiesis in aplastic anaemia has demonstrated some unique features of dyserythropoiesis at the ultrastructural level, which contribute to understanding of the morphological features which are seen in the light microscope. The findings provide further evidence for the presence of qualitative defects in erythropoiesis in aplastic conditions. The alterations seen included bi- and multinucleated cells, intercellular bridges containing microtubules, internuclear chromatin bridges, irregular nuclear shapes, juxta-nuclear and peripheral cisternal structures, ringed sideroblasts, a diversity of intranuclear inclusions, nuclear clefts in both eu- and heterochromatin, and a variety of anomalies of the nuclear membrane. The significance of the occurrence of these anomalies in aplastic anaemia is considered and the role of the nuclear membrane and of endoplasmic reticulum in the pathogenesis of aplastic anaemia is discussed.