Nuclear Chromatin Structure Research Articles

Hyperthermia does not affect rejoining of DNA double-strand breaks in a cell-free assay

Purpose : Heat radiosensitization is poorly understood but is believed to be caused by an inhibition in the repair of radiation-induced DNA lesions. This inhibition in DNA repair may be caused either by direct heat inactivation of repair enzymes, or by heat-induced protein denaturation that leads to their precipitation onto nuclear chromatin structures, generating a barrier that prevents repair enzymes from reaching the damage sites. Material and methods : A previously described (Ganguly and Iliakis, Int J Radiat Biol 1995, 68, 447-457) cell-free assay was introduced to evaluate rejoining of radiation-induced DNA double-strand breaks (dsb) in heated (45.5°C, 20 min) nuclei prepared from A549 cells, in reactions assembled with extracts of non-heated and non-irradiated HeLa cells. The assay allowed the functional evaluation of the effect of precipitated nuclear protein on dsb rejoining. By combining heated nuclei with extracts of non-heated cells the assay avoided complications that would otherwise arise when intact cells are studied, where both nuclear structures and repair factors are heated and therefore potentially altered. Results : It was observed that exposure of A549 cells to 45.5°C for 20 min caused a 50% increase in the relative protein content of isolated nuclei but had no effect on the in vitro rejoining of dsb. In agreement with earlier reports, a greatly reduced rate of dsb rejoining was observed either in intact A549 or HeLa cells after exposure to heat. Conclusions : The results indicate that an increased retention of proteins in heated nuclei is not necessarily associated with an inhibition of dsb rejoining. While the in vitro system may only reproduce certain aspects of the in vivo conditions, the results suggest that protein accretion as a mechanism of heat radiosensitization requires further testing using functional assays.

Significance of protein kinase CK2 nuclear signaling in neoplasia.

Many stimuli play a role in influencing the structure and function of chromatin and nuclear matrix through post-translational modifications of the component proteins in these dynamic structures. We propose that the protein serine/threonine kinase CK2 (formerly casein kinase II) is one such agent that is involved in signal transduction in the nuclear matrix and chromatin in response to a variety of stimuli. Protein kinase CK2 appears to undergo rapid modulations in its association with nuclear matrix and nucleosomes in response to mitogenic signals and is involved in the phosphorylation of a variety of intrinsic proteins in these structures depending on the state of genomic activity. In addition, its association or loss from the nuclear matrix may also influence the apoptotic activity in the cell. CK2 has been found to be dysregulated in virtually all the neoplasias examined and nuclear association appears to be an important facet of its expression in tumor cells. We hypothesize that CK2 provides a functional paradigm linking the nuclear matrix and chromatin structures. Identification of precise loci of action of CK2 in these structures and how they influence the morphological appearance of the nucleus under normal and abnormal growth conditions would be an important future direction of investigation. J. Cell. Biochem. Suppl. 35:130-135, 2000. Published 2001 Wiley-Liss, Inc.

Localization of radiation-induced chromosomal breakpoints along human chromosome 1 using a combination of G-banding and FISH

Purpose : To determine the exact location of radiation-induced chromosomal breakpoints along the euchromatic or heterochromatic regions: G-light and G-dark bands, respectively. Materials and methods : The distribution of radiation-induced chromosomal breakpoints was scored in human lymphocytes irradiated in vitro with 3 Gy of gamma-radiation. Image analysis was applied to combine G-banded and FISH-painted images of the human chromosome 1. Results : A total of 195 chromosomal breakpoints in 176 cells with structural chromosomal aberrations was used for the present analysis. Radiation-induced breakpoints were found to be distributed randomly with respect to the p or q arms of chromosome 1 and specific band or band length, but more breakpoints were mapped to G-light than to G-dark bands, the difference being statistically significant. Conclusions : The results can well be interpreted in terms of concepts of existing models of nuclear architecture, chromatin structure and transcriptional activities of the chromatin, which can influence the induction of primary chromosomal aberrations by gamma-rays. Differential repair of randomly produced primary aberrations may also explain the non-random distribution of radiation-induced breakpoints.

Changes of chromatin condensation in one patient with ataxia telangiectasia disorder: a structural study.

Differential scanning calorimetry and quantitative fluorescence microscopy have been employed to characterize the structure and organization of in situ chromatin in lymphoblastoid cells obtained from one ataxia telangiectasia (A-T) patient and one healthy family member. The proven capability of these biophysical techniques to measure changes of chromatin condensation directly inside the cells makes them very powerful in studying the eventual structural changes associated with the appearance of a pleiotropic genetic disorder such as ataxia telangiectasia. A-T syndrome is genetically heterogeneous and can be induced by different mutations of a single gene. The aim of this work is to determine whether the genetic mutation exhibited by the A-T patient of this study may be associated with modifications of chromatin structure and organization. Both the calorimetric and the fluorescence microscopy results acquired on cells from the A-T patient show that the structure and distribution of nuclear chromatin in situ change considerably with respect to the control. A significant decondensation of the nuclear chromatin is in fact associated with the appearance of the A-T disorder in the A-T patient under analysis, together with a rearrangement of the chromatin domains inside the nucleus.

DNA replication in quiescent cell nuclei: regulation by the nuclear envelope and chromatin structure.

Quiescent nuclei from differentiated somatic cells can reacquire pluripotence, the capacity to replicate, and reinitiate a program of differentiation after transplantation into amphibian eggs. The replication of quiescent nuclei is recapitulated in extracts derived from activated Xenopus eggs; therefore, we have exploited this cell-free system to explore the mechanisms that regulate initiation of replication in nuclei from terminally differentiated Xenopus erythrocytes. We find that these nuclei lack many, if not all, pre-replication complex (pre-RC) proteins. Pre-RC proteins from the extract form a stable association with the chromatin of permeable nuclei, which replicate in this system, but not with the chromatin of intact nuclei, which do not replicate, even though these proteins cross an intact nuclear envelope. During extract incubation, the linker histones H1 and H1(0) are removed from erythrocyte chromatin by nucleoplasmin. We show that H1 removal facilitates the replication of permeable nuclei by increasing the frequency of initiation most likely by promoting the assembly of pre-RCs on chromatin. These data indicate that initiation in erythrocyte nuclei requires the acquisition of pre-RC proteins from egg extract and that pre-RC assembly requires the loss of nuclear envelope integrity and is facilitated by the removal of linker histone H1 from chromatin.

Silencing at Drosophila telomeres: nuclear organization and chromatin structure play critical roles.

Transgenes inserted into the telomeric regions of Drosophila melanogaster chromosomes exhibit position effect variegation (PEV), a mosaic silencing characteristic of euchromatic genes brought into juxtaposition with heterochromatin. Telomeric transgenes on the second and third chromosomes are flanked by telomeric associated sequences (TAS), while fourth chromosome telomeric transgenes are most often associated with repetitious transposable elements. Telomeric PEV on the second and third chromosomes is suppressed by mutations in Su(z)2, but not by mutations in Su(var)2-5 (encoding HP1), while the converse is true for telomeric PEV on the fourth chromosome. This genetic distinction allowed for a spatial and molecular analysis of telomeric PEV. Reciprocal translocations between the fourth chromosome telomeric region containing a transgene and a second chromosome telomeric region result in a change in nuclear location of the transgene. While the variegating phenotype of the white transgene is suppressed, sensitivity to a mutation in HP1 is retained. Corresponding changes in the chromatin structure and inducible activity of an associated hsp26 transgene are observed. The data indicate that both nuclear organization and local chromatin structure play a role in this telomeric PEV.

Mechanisms and Control of Embryonic Genome Activation in Mammalian Embryos

Activation of transcription within the embryonic genome (EGA) after fertilization is a complex process requiring a carefully coordinated series of nuclear and cytoplasmic events, which collectively ensure that the two parental genomes can be faithfully reprogrammed and restructured before transcription occurs. Available data indicate that inappropriate transcription of some genes during the period of nuclear reprogramming can have long-term detrimental effects on the embryo. Therefore, precise control over the time of EGA is essential for normal embryogenesis. In most mammals, genome activation occurs in a stepwise manner. In the mouse, for example, some transcription occurs during the second half of the one-cell stage, and then a much greater phase of genome activation occurs in two waves during the two-cell stage, with the second wave producing the largest onset of de novo gene expression. Changes in nuclear structure, chromatin structure, and cytoplasmic macromolecular content appear to regulate these periods of transcriptional activation. A model is presented in which a combination of cell cycle-dependent events and both translational and posttranslational regulatory mechanisms within the cytoplasm play key roles in mediating and regulating EGA.

Effects of polyamines on higher-order folding of in situ chromatin.

Modifications of the higher-order chromatin structure induced by polyamines have been quantitatively investigated in situ through a non-invasive biophysical approach using Differential Scanning Calorimetry and Quantitative Fluorescence Microscopy. Calorimetric and intensitometric profiles have been acquired for samples of native thymocytes, alternatively suspended in buffers, with or without natural polyamines (spermine and spermidine). The results here reported show that the structure and distribution of nuclear chromatin in situ considerably change upon the ionic composition of the environment. A quantitative analysis of this data and a comparison with previous results obtained from isolated chromatin fibers was carried out. Finally, an inverse relationship between chromatin condensation and nuclear volume was observed.

Effects of heat stress on mouse testicular cells and sperm chromatin structure.

Scrotal regions of mice were exposed to a 38.0, 40.0, or 42.0 degrees C (+/-0.1) H2O bath for 60 minutes to determine the effects of elevated temperatures on testicular cells and sperm chromatin structure. Mice were killed on various days after exposure, and ratios of acridine orange-stained testicular cell populations were determined by flow cytometry. Testicular weights of mice exposed to 42.0 degrees C decreased significantly day 1 (P < 0.01) through 35 (P < 0.001). Also, a significant relative decrease in testicular haploid cells was seen on days 3-35 (P < 0.001) with a corresponding increase in the diploid population (P < 0.001). Testicular analyses of mice exposed to 38.0 degrees C were not significantly different from control values. Testis weights of mice exposed to 40.0 degrees C were not affected, but a relative decrease in percent haploid cells occurred on days 11 and 14 (P < 0.001). The sperm chromatin structure assay (SCSA) was used to measure the susceptibility of cauda epididymal sperm DNA to in situ denaturation at low pH. Caudal epididymides of mice exposed to 42.0 degrees C had no sperm. Caudal epididymal sperm from mice exposed to 40.0 degrees C were most susceptible to acid-induced DNA denaturation on days 3 (P < 0.05), 7, 11, and 14 (all P < 0.001). The 38.0 degrees C exposed mice showed some minor sperm chromatin abnormalities at later time points (days 11-35). When compared to sperm head morphology measurements, SCSA parameters were more sensitive indicators of heat-induced sperm abnormalities. These results show that mouse spermatogenesis is disrupted by scrotal exposure to environmental temperatures several degrees over normal physiological temperature and, of more biological interest, that some thermal ranges above normal allowed production of sperm with compromised nuclear chromatin structure.

AMELIORIATION OF CHEMICALLY-INDUCED HEPATOCYTE INJURY BY CYCLOSPORINE A

Cyclosporine A, beside its current applications, possesses potential hepatoprotective effects. This study was directed to investigate the effect of Cyclosporine A pretreatment on hepatic injury due to carbon tetrachloride (CCl 4) and D-galactosamine. Rats were injected by two successive doses of Cyclosporine A (5mgkg −1day −1). Six hours after the second dose, 1mlkg −1of CCl 4was administered i.p. Effects associated with Cyclosporine A pretreatment were examined by using isolated hepatocytes and hepatocytes that were immobilized and continuously perfused. D-Galactosamine (5m M) was added directly to the perfusion medium. After isolation, hepatocytes were examined histologically by light and electron microscopy, immobilized and perfused for further metabolic functional activity evaluation. Cyclosporine A pretreatment in vivoproduced hepatoameliorative effects of various degrees which were statistically significant as manifested by: (1) an increased trypan blue exclusion after CCl 4; (2) an improved ureagenesis after CCl 4; (3) a reduction in the lipid droplets accumulation in the cytoplasm produced by CCl 4administration; (4) well preserved cytoplasmic organelles as mitochondria, endoplasmic reticulum ER, nuclear chromatin structures that were altered by CCl 4; and (5) an increased hepatocytes survival in the agarose gel matrix, reduction of LD leakage and improvement of ureagenesis after D-galactosamine addition to the perfusion medium. The beneficial effect of Cyclosporine A pretreatment in modifying hepatotoxicity of chemical insults merits further studies.

Nuclear image analysis of immunohistochemically stained cells in breast carcinomas.

Hitherto, the relationship between malignancy-associated morphological features in single tumour cells and the expression of markers indicating functional properties of these cells remained widely unknown. This study was aimed at describing differences in the size, shape and chromatin structure between tumour cells with different marker expression for progesterone receptors (PgR) and p53. Two series of breast cancers, consisting of 50 PgR-positive, and 39 p53-negative and 49 p53-positive mammary carcinomas, were investigated. The immunohistochemical staining was performed on paraffin sections using 3-amino-9-ethylcarbazole as the chromogenic substrate. By means of a cytometry workstation equipped with a computer-controlled motorised scanning stage, about 500 positive and negative tumour cells in each case were localised in the microscope and categorised by a scoring system for their staining intensity. After destaining, the tissue sections were Feulgen-stained. Then, all the tumour cells were relocated automatically and analysed by high resolution image cytometry. Among the numerous size, shape, and texture features used in the system, several variables of the nuclear contour and chromatin structure were found to be significantly different between the positive and negative tumour cell populations. Nuclei without PgR had more malignancy-associated morphological features than PgR-positive cells. Whereas p53-negative nuclei had a higher degree of regularity, their positive counterparts exhibited higher DNA ploidy values.

A developmentally modulated chromatin structure at the mouse immunoglobulin kappa 3' enhancer.

Transcription of the mouse immunoglobulin kappa gene is controlled by two enhancers: the intronic enhancer (Ei) that occurs between the joining (J kappa) and constant (C kappa) exons and the 3' enhancer (E3') located 8.5 kb downstream of the gene. To understand the role of E3' in the activation of the mouse immunoglobulin kappa gene, we studied its chromatin structure in cultured B-cell lines arrested at various stages of differentiation. We found that 120 bp of the enhancer's transcriptional core becomes DNase I hypersensitive early in B-cell development. Genomic footprinting of pro-B and pre-B cells localized this chromatin alteration to B-cell-specific protections at the region including the direct repeat (DR) and the sequence downstream of the DR (DS), the PU.1-NFEM-5 site, and the core's E-box motif, identifying bound transcription factors prior to kappa gene rearrangement. Early footprints were, however, not detected at downstream sites proposed to play a negative role in transcription. The early chromatin structure persisted through the mature B-cell stage but underwent a dramatic shift in plasma cells, correlating with the loss of guanosine protection within the DR-DS junction and the appearance of novel footprints at a GC-rich motif upstream and the NF-E1 (YY1/delta)-binding site downstream. Gel shift analysis demonstrated that the DR-DS junction is bound by a factor with properties similar to those of BSAP (B-cell-specific activator protein). These results reveal developmental-stage-specific changes in the composition of nuclear factors bound to E3', clarify the role of factors that bind constitutively in vitro, and point to the differentiation of mature B cells to plasma cells as an important transitional point in the function of this enhancer. The observed changes in nuclear factor composition were accompanied by the rearrangement of positioned nucleosomes that flank the core region, suggesting a role for both nuclear factors and chromatin structure in modulating kappa E3' function during B-cell development. The functional implications of the observed chromatin alterations are discussed in the context of recent studies on kappa E3' and the factors that bind to it.

Cytophotometric and biochemical analyses of DNA in pentaploid and diploid Agave species

Nuclear DNA content, chromatin structure, and DNA composition were investigated in four Agave species: two diploid, Agave tequilana Weber and Agave angustifolia Haworth var. marginata Hort., and two pentaploid, Agave fourcroydes Lemaire and Agave sisalana Perrine. It was determined that the genome size of pentaploid species is nearly 2.5 times that of diploid ones. Cytophotometric analyses of chromatin structure were performed following Feulgen or DAPI staining to determine optical density profiles of interphase nuclei. Pentaploid species showed higher frequencies of condensed chromatin (heterochromatin) than diploid species. On the other hand, a lower frequency of A-T rich (DAPI stained) heterochromatin was found in pentaploid species than in diploid ones, indicating that heterochromatin in pentaploid species is made up of sequences with base compositions different from those of diploid species. Since thermal denaturation profiles of extracted DNA showed minor variations in the base composition of the genomes of the four species, it is supposed that, in pentaploid species, the large heterochromatin content is not due to an overrepresentation of G-C repetitive sequences but rather to the condensation of nonrepetitive sequences, such as, for example, redundant gene copies switched off in the polyploid complement. It is suggested that speciation in the genus Agave occurs through point mutations and minor DNA rearrangements, as is also indicated by the relative stability of the karyotype of this genus. Key words : Agave, DNA cytophotometry, DNA melting profiles, chromatin structure, genome size.

Preferential targeting of oxidative base damage to internucleosomal DNA.

The structure of nuclear chromatin may limit the accessibility of carcinogenic agents to DNA. In the case of oxidative DNA strand cleavage mediated by the physiologically relevant iron chelate, iron-ADP, histone-associated nucleosomal DNA is protected while internucleosomal DNA is susceptible to damage. We now find that the distribution of iron-ADP-generated 8-hydroxydeoxyguanosine, a potentially mutagenic oxidative base change, shows relative targeting to internucleosomal sites (3.5-fold increased oxidative modification of internucleosomal compared with nucleosomal DNA as the minimal degree of enrichment). In contrast, iron-EDTA, which generates hydroxyl radical in the 'fluid phase', does not target internucleosomal DNA. Thus, physiologic iron chelates may promote site-specific damage and thereby be relevant to mechanisms of iron-dependent oxidative mutagenesis and carcinogenesis.

Rapid reorganization of microtubular cytoskeleton accompanies early changes in nuclear ploidy and chromatin structure in postmitotic cells of barley leaves infected with powdery mildew

Post-mitotic epidermal cells of barley leaves were found to contain, in addition to cortical microtubules (CMTs), distinct arrays of endoplasmic microtubules (EMTs). These encircle nuclei and continuously merge into the CMT arrays that underly the plasmalemma. Detailed three-dimensional reconstruction of both types of MTs during fungal infection showed that profound and very rapid MT rearrangements occurred especially in the case of incompatible (resistant) barley-powdery mildew genotype combination. The most early MT responses, followed by their subsequent complete disintegration, were recorded around nuclei. These events might be relevant for the induction of such nuclear processes as onset of DNA synthesis and nuclear chromatin condensation. Observed pattern of early infection events, as well as less prominent responses in the case of compatible (susceptible) barley-powdery mildew genotype combination, both findings suggest that rapid reorganization of the MT cytoskeleton could be involved in recognition of the fungus by host cells and in the initiation of resistance responses in barley leaves. We hypothesize that the integrity and dynamics of the MT cytoskeleton, especially of its perinuclear part, might participate in control mechanisms involved in activation of resistance genes.

Chronic psychosocial stress induces morphological alterations in hippocampal pyramidal neurons of the tree shrew

The effect of sustained psychosocial stress on the morphology of hippocampal pyramidal neurons was analysed in male tree shrews after 14, 20, and 28 days of social confrontation. A variety of physiological changes such as constantly elevated levels of urinary cortisol and norepinephrine and reduced body weight, which are indicative of chronic stress were observed in the subordinate, but not in the dominant males. Light microscopic analysis of Nissl-stained hippocampal sections showed that the staining intensity of the nucleoplasm in the CA1 and CA3 pyramidal neurons was increased after prolonged psychosocial stress, indicating a change in the nuclear chromatin structure. These alterations were observed only in subordinate animals and increased in a time dependent manner in accordance with the length of the stress period. There was, however, neither a reduction in density nor a degeneration of pyramidal neurons in chronically stressed animals. Mechanisms which may possibly account for the observed alterations are discussed.

Nuclear DNA analysis of maize seedlings treated with the triazole fungicide, triticonazole

AbstractMaize kernels were treated with the fungicide triticonazole (RP‐727), belonging to the triazole family. The nuclear DNA content was analyzed in various maize plant organs by using flow cytometry. Two fluorochromes with different DNA binding mechanisms were used for probing nuclear DNA and chromatin structure. Results indicated nuclear alterations with the use of triticonazole and the alterations observed were different in the various tissues analyzed. Active meristematic plant organs, such as root tip, did not show any significant change in nuclear DNA, but chromatin structure was altered with increasing concentrations of fungicide. Stem and mesocotyl showed both DNA and chromatin condensation changes with triticonazole concentration, but the trends observed in these two plant organs were opposite. The magnitude of the alterations was minute in the different plant organs studied. These alterations do not appear to be deleterious for normal plant development.

Nuclear architecture supports integration of physiological regulatory signals for transcription of cell growth and tissue-specific genes during osteoblast differentiation.

During the past several years it has become increasingly evident that the three-dimensional organization of the nucleus plays a critical role in transcriptional control. The principal theme of this prospect will be the contribution of nuclear structure to the regulation of gene expression as functionally related to development and maintenance of the osteoblast phenotype during establishment of bone tissue-like organization. The contributions of nuclear structure as it regulates and is regulated by the progressive developmental expression of cell growth and bone cell related genes will be examined. We will consider signalling mechanisms that integrate the complex and interdependent responsiveness to physiological mediators of osteoblast proliferation and differentiation. The focus will be on the involvement of the nuclear matrix, chromatin structure, and nucleosome organization in transcriptional control of cell growth and bone cell related genes. Findings are presented which are consistent with involvement of nuclear structure in gene regulatory mechanisms which support osteoblast differentiation by addressing four principal questions: 1) Does the representation of nuclear matrix proteins reflect the developmental stage-specific requirements for modifications in transcription during osteoblast differentiation? 2) Are developmental stage-specific transcription factors components of nuclear matrix proteins? 3) Can the nuclear matrix facilitate interrelationships between physiological regulatory signals that control transcription and the integration of activities of multiple promoter regulatory elements? 4) Are alterations in gene expression and cell phenotypic properties in transformed osteoblasts and osteosarcoma cells reflected by modifications in nuclear matrix proteins? There is a striking representation of nuclear matrix proteins unique to cells, tissues as well as developmental stages of differentiation, and tissue organization. Together with selective association of regulatory molecules with the nuclear matrix in a growth and differentiation-specific manner, there is a potential for application of nuclear matrix proteins in tumor diagnosis, assessment of tumor progression, and prognosis of therapies where properties of the transformed state of cells is modified. It is realistic to consider the utilization of nuclear matrix proteins for targeting regions of cell nuclei and specific genomic domains on the basis of developmental phenotypic properties or tissue pathology.

Subclinical Human Immunodeficiency Virus-Related Changes in Oral Mucosa Shown by Image Analysis of Tongue Smears

There is evidence that certain lesions of the oral mucosa, such as hairy leukoplakia (HL), in patients seropositive for human immunodeficiency virus correlate with the subsequent development of acquired immune deficiency syndrome. The authors suggest that HL is a final manifestation of alterations that gradually develop after HIV infection. To recognize inapparent early subclinical changes in oral mucosa, the authors applied methods of digital image analysis to investigate tongue smears from healthy control subjects and immunosuppressed patients after chemotherapy and HIV infection. Their studies concentrated on nuclear morphologic features and chromatin structure. The results obtained with a large set of subvisual parameters indicated significant differences in nuclear and chromatin features between the smear patterns of investigated groups. One important implication of these studies is that computerized image analysis of simply prepared tongue smears enables one to recognize subvisual HIV-related changes before clinical evidence of HL appears.

Glycolytic enzymes as DNA binding proteins

1. 1. Numerous studies have demonstrated the presence of at least four glycolytic enzymes in the nuclear compartment of several cell systems. 2. 2. These include, lactate dehydrogenase, phosphoglycerate kinase, aldolase and glyceraldehyde-3-phosphate dehydrogenase. 3. 3. In some cases the glycolytic enzymes found in the nuclei were a modified form from that found in the cytoplasmic counterpart. 4. 4. In all four eases, the nuclear form of these glycolytic enzymes has been reported to bind DNA. 5. 5. Although none of these enzymes interact with a specific target DNA sequence, their association with DNA may play a role in transcription and replication of DNA through general stabilization of the nuclear matrix or chromatin structure. 6. 6. The present review aims to summarize the current understanding of this phenomenon and to examine the role of the DNA-binding activities of the glycolytic enzymes in cell growth and differentiation.