Perichromatin fibrils and chromatin ultrastructural pattern

Chromatin structure in situ: the contribution of DNA ultrastructural cytochemistry

Ultrastructural studies conducted in situ using conventional transmission electron microscopy have had relatively little impact on defining the structural organization of chromatin. This is due to the fact that in routine transmission electron microscopy, together with the deoxyribonucleoprotein, many different intermingled substances are contrasted, masking the ultrastructure of chromatin. By selective staining of DNA in thin sections, using the Feulgen-like osmium-ammine reaction, these drawbacks have been overcome and worthwhile data have been obtained both on the gross morphology and the ultrastructural-functional organization of chromatin in situ. In the present study these results are reviewed and discussed in light of recent achievements in both interphase nuclear chromatin compartmentalization in interphase nuclei and in the structural organization of chromatin fibers in transcriptionally active and inactive chromatin.

The perichromatin region: a functional compartment in the nucleus that determines large-scale chromatin folding

The perichromatin region has emerged as an important functional domain of the interphase nucleus. Major nuclear functions, such as DNA replication and transcription, as well as different RNA processing factors, occur within this domain. In this review, we summarize in situ observations regarding chromatin structure analysed by transmission electron microscopy and compare results to data obtained by other methods. In particular, we address the functional architecture of the perichromatin region and the way chromatin may be folded within this nucleoplasmic domain.

The nuclear matrix: a structural milieu for genomic function

While significant progress has been made in elucidating molecular properties of specific genes and their regulation, our understanding of how the whole genome is coordinated has lagged behind. To understand how the genome functions as a coordinated whole, we must understand how the nucleus is put together and functions as a whole. An important step in that direction occurred with the isolation and characterization of the nuclear matrix. Aside from the plethora of functional properties associated with these isolated nuclear structures, they have enabled the first direct examination and molecular cloning of specific nuclear matrix proteins. The isolated nuclear matrix can be used for providing an in vitro model for understanding nuclear matrix organization in whole cells. Recent development of high-resolution and three-dimensional approaches for visualizing domains of genomic organization and function in situ has provided corroborative evidence for the nuclear matrix as the site of organization for replication, transcription, and post-transcriptional processing. As more is learned about these in situ functional sites, appropriate experiments could be designed to test molecular mechanisms with the in vitro nuclear matrix systems. This is illustrated in this chapter by the studies of nuclear matrix-associated DNA replication which have evolved from biochemical studies of in vitro nuclear matrix systems toward three-dimensional computer image analysis of replication sites for individual genes.

The nuclear matrix: a heuristic model for investigating genomic organization and function in the cell nucleus

Despite significant advances in deciphering the molecular events underlying genomic function, our understanding of these integrated processes inside the functioning cell nucleus has, until recently, met with only very limited success. A major conundrum has been the "layers of complexity" characteristic of all cell structure and function. To understand how the cell nucleus functions, we must also understand how the cell nucleus is put together and functions as a whole. The value of this neo-holistic approach is demonstrated by the enormous progress made in recent years in identifying a wide variety of nuclear functions associated with the nuclear matrix. In this article we summarize basic properties of in situ nuclear structure, isolated nuclear matrix systems, nuclear matrix-associated functions, and DNA replication in particular. Emphasis is placed on identifying current problems and directions of research in this field and illustrating the intrinsic heuristic value of this global approach to genomic organization and function.

Localization of heterogeneous nuclear ribonucleoprotein in the interphase nuclear matrix core filaments and on perichromosomal filaments at mitosis

Although heterogeneous nuclear RNA (hnRNA) has been localized to the core filament substructure of the nuclear matrix, its precise location in the filament network has been unknown. The fA12 monoclonal antibody can localize, at high resolution, hn ribonucleoproteins (hnRNPs) and, presumably, hnRNA. Gold bead immunolabeling of resinless electron microscopy sections showed the fA12 antigens were in the fibrogranular material enmeshed in the filament network and not in the filaments themselves. At mitosis, hnRNP antigens became dispersed into a halo surrounding the chromosomes and spindle poles. Immunogold staining showed fA12 stained fibrogranular material associated with perichromosomal and pericentriolar filaments distinct from the mitotic spindle fibers. fA12 also labeled the midbody remaining after cytokinesis.

A model of chromatin-dependent DNA replication sequences based on the decondensation units hypothesis

A model of chromatin-dependent DNA replication sequences was developed on the previously reported "decondensation units" hypothesis and its kinetic properties were examined by way of calculating various numerical indices using a Monte Carlo procedure. The model has much in common with the previous one but a fundamental difference is that the unit is assumed to consist of linearly arranged H-, D-, A- and S-zones each containing genes of different functional categories which are called H-, D-, A- and S-genes, respectively. The units are decondensed by the action of D-factors, i.e. decondensation factors, from H-zone to the end of S-zone and the genes in decondensed regions release signals to produce housekeeping enzymes, D-factors, A-factors and S-factors. These products are stored and at the same time degraded. A-factors activate replication origins in the decondensed regions and S-factors induce DNA synthesis at the activated origins. Replicated DNA is recondensed and gene activities are shut down in the recondensed chromatin. The factors are produced under the control of chromosome cycle and in turn affect chromosomes. Thus, dual control mechanism operates as Mazia and Prescott have argued. Biochemical and cytogenetic basis of this model was reviewed briefly and some results of simulation presented which include DNA synthesis rate vs. DNA content relationships. An outstanding characteristic of the model is the constancy of cellular state in A-subphase located in the late G1.

Nuclear morphology of transitional keratinocytes in normal human epidermis

Transitional keratinocytes (TK) of normal interfollicular human epidermis were studied by electron microscopy to provide more information on the ultrastructural nuclear and nucleolar changes during physiological keratinization. The results revealed that TK contained condensed nuclei in the initial stage, degraded nuclei in the advanced stage, and nuclear remnants in the late stage of their transformation into cornified cells. The condensed nuclei were essentially characterized by ultrastructural changes generally considered to reflect the cessation of RNA synthesis. The focal increase of density and the structural disintegration observed in the degraded nuclei of TK are apparently characteristic morphological features of degradation of nucleoproteins in these cells. Nuclear remnants contained altered nuclear envelope or similar structures and clumps of dense fibrillar material. Similar clumps of dense fibrils were present in the cytoplasm of both the TK with compact nuclear remnants and the TK with structural disintegration. This finding suggests that some dense fibrillar material of structurally disintegrating nuclei of TK is transported into the cytoplasm of these cells.

The aging of the endocrine pancreas of the rat. I. Parameters of cell proliferation

Morphometrical analysis of the endocrine pancreas of senile 30-month-old rats revealed that the volume density as well as the numeric density of islets of Langerhans were much lower than in 24-month-old rats, which coincided with a much higher percentage of pycnotic nuclei in islet cells. The proportion and localization of the different categories of endocrine cells (A, B, D and PP) remained however unchanged with aging. The apparent problem of cell renewal observed in vivo in the very old age was detected earlier in vitro by tritiated thymidine incorporation. Such experiments showed that 24-month-old islet cells had a decreased labelling index when compared to 3-month-old cells. The proliferation capacity of the old cells could be partially increased by changing the serum concentration or type. Similarly as being more sensitive to serum factors, these cells underwent also more pronounced negative influence of high oxygen pressure on replication. A stereological analysis of the ultrastructure of non-degenerated B-cell nuclei revealed that with age, the relative volume of the condensed chromatin increased progressively at the expense of the dispersed form. This suggests that the still functioning senile B-cells could reduce their transcriptional activity.

Changes in structure and composition of lymphocyte nuclei during mitogenic stimulation

Nuclei of lymphocytes stimulated in vitro with concanavalin A (Con A) were classified into three morphotypes: I--unstimulated; II--partially stimulated; III--fully stimulated, lymphoblastic nuclei. During the Con A-induced change from morphotype I to III nuclear volume increased up to sixfold, due to a near 10-fold increase in the interchromatinic region. At the same time, condensed chromatin rose in volume by only about 1.5-fold and became disaggregated in to small clumps. Regressive EDTA-uranyl staining demonstrated a large increase in interchromatinic fibrillar material in morphotypes II and III. Nuclear matrices isolated from stimulated murine lymphocytes showed structures comparable to the interchromatinic region of the morphotypes. The Con A-stimulated change in nuclear structure preceded onset of DNA replication and was unaffected by hydroxyurea or cytosine arabinoside. Cycloheximide blocked the structural change, even when given 20 hr after Con A. Autoradiography after [3H]leucine showed incorporation of label in the interchromatinic region of morphotype II and III nuclei, much of which remained stable during a 48-hr chase period. Nuclear structural activation was inhibited by alpha-amanitin but a significant stable nuclear RNA fraction was not detected. We conclude that an important event in lymphocyte activation is extensive synthesis of stable proteinaceous interchromatinic matrix which may be involved in chromatin remodeling and DNA replication and/or transcription.

High-resolution autoradiographic study on the presence of chromatin structures within interchromatin granule conglomerations

In Ehrlich ascites tumour cell nuclei ledakrin (1-nitro-9/3'-dimethylpropyloamine/acridine-2 HCl) induces condensation and margination of chromatin, compaction and segregation of nucleolar components and conglomeration of chromatin granule clusters. Localization of DNA in nuclei of the cells labelled with 3H-thymidine and subsequently treated with ledakrin is studied using high-resolution autoradiography. Besides strong labelling of condensed chromatin some radioactivity is associated with IG conglomerations. Possible role of chromatin fibrils in the formation of conglomerations of IG is discussed.

Morphology of nuclear ribonucleoproteins in the early period of liver regeneration after irradiation

Cytochemical study of hepatocytes nuclei of the liver irradiated with a dose of 650 rad and irradiated after partial hepatectomy was performed. Morphological exponents of the intensive synthesis of preribosomal RNA in the nucleolus, as well as the transcription of heterogeneous RNA contained in perichromatin fibrils were revealed under the ionizing radiation effect. The behavior of perichromatin granules in the course of the experiment suggests delay in the transport of messenger RNA to cytoplasm, influenced by gamma radiation. Nuclear bodies were observed very often in nuclei of hepatocytes of irradiated animals.

Chromatin condensation in isolated rat hepatocyte nuclei induced by ribonuclease treatment

Ribonuclease treatment of isolated rat hepatocyte nuclei induced a 75% solubilization in hnRNA, a reduction of the quantity of perichromatin fibrils, and a marked condensation of chromatin.

Methods in ultrastructural cytochemistry of the cell nucleus

The electron microscopical study of the cell nucleus as observed in thin sections requires the use of cytochemical methods because of the intricate pattern of the nuclear components. The in situ techniques based on electron staining and enzymatic digestion are reviewed, excluding autoradiography, cytoenzymology and immunocytochemistry. A tentative classification has been adopted according to the chemical nature of the revealed component. Thus, the staining procedures for the nucleoproteins in general, for both nucleic acids, for the proteins, and finally for the deoxyribonucleoproteins and DNA are considered separately. 1--Stains for the nucleoproteins include simple reagents such as the uranyl and lead salts which are largely used in electron microscopy but are of limited specificity. 2--A variety of methods, some of them specific, is available for the simultaneous visualization of DNA and RNA which is based on common properties: basophilia, ability to bind diaminoacridines, presence of hydroxyl groups. However, due to the recent development of specific and preferential methods for each nucleic acid, we feel that among the older methods, only rapid and simple procedures for the detection of both nucleic acids remain of interest. 3--Proteins being ubiquitous, the useful techniques must reveal subsets within the total nuclear proteins. Apart from some endogeneous enzymes, basic proteins -- practically histones -- so far represent the only group for the detection of which reliable methods exist. 4--Several techniques developed recently are available for the specific detection of DNA. In favourable cases, methods derived from the Feulgen reaction allow its visualization at a molecular level. In addition, standard procedures for the preparation of mammalian cells and tissues are described. Each staining method is at least briefly discussed, but emphasis has been placed on a small number of techniques described in detail. They comprise the EDTA regressive stain for the ribonucleoproteins, several reactions of the basic proteins and the Feulgen-like osmium ammine reaction for DNA.