Nucleolar DNA Research Articles

Tumor doubling time, argyrophil nucleolar organizer regions and nuclear DNA content of primary lung cancer and prognostic assessment

Tumor doubling time, argyrophil nucleolar organizer regions and nuclear DNA content of primary lung cancer and prognostic assessment

Three-dimensional co-localization of nucleolar argyrophilic components and DNA in cell nuclei by confocal microscopy.

Silver dots deposited specifically on proteins of the nucleolar organizer regions (Ag-NOR proteins) after a one-step silver staining technique were visualized in cells in culture, in cells in smears, and in tissue sections, with a scanning laser confocal microscope working in the reflectance mode. After specific labeling of DNA with the fluorescent dye chromomycin A3, DNA and silver dots could be observed either individually or simultaneously. Therefore, it was possible to study the three-dimensional organization of nucleolar silver-stained structures relative to DNA with a high X, Y, and Z resolution. Our results showed that the argyrophilic components are organized as a twisted necklace structure within interphase nucleoli of cells in culture. We also demonstrated a striking three-dimensional symmetric disposition of NORs within the two sets of chromosomes in telophase cells. Similar results were obtained for cells in smears, although their three-dimensional organization was somewhat disturbed due to air-drying. We also demonstrated that silver dots cannot be visualized in the reflectance mode within sections of paraffin-embedded tissues. However, their simultaneous demonstration in non-confocal transmitted light, together with that of DNA in confocal mode, appeared very useful to study their localization within nuclei and mitotic chromosomes.

Nucleolus-like morphology produced during the in vitro reassociation of nucleolar components.

Nucleoli, the sites of rRNA synthesis, rRNA processing, and the assembly of ribosomes, are dynamic organelles that, in most cells, disperse and reform during mitosis. The mechanisms that regulate nucleolar formation are unknown as is the relationship between nucleolar morphology and the pathway of ribosome biogenesis. In this report we describe the in vitro formation of nucleolus-like particles (NLPs) from soluble extracts of nucleoli. NLPs, which reached sizes comparable to nucleoli (1-3 microns), were found to contain 40% of the nucleolar DNA, RNA, and protein. The ultrastructure of NLPs resembled that of a number of in vivo structures including compact nucleoli, prenucleolar bodies, and pseudonucleoli. The particles were composed of two morphologically distinct regions. The core resembled the dense fibrillar component (DFC) of nucleoli while the cortex resembled the granular component (GC) of nucleoli. The cortex of NLPs contained numerous 15-20 nm osmophilic granules that resembled the preribosomes found in the GC of nucleoli. The distribution of nucleolar proteins in NLPs also resembled that in nucleoli. BN46/51, a component of the GC of nucleoli, was restricted to the GC-like cortex of NLPs. A mAb that bound to the DFC of nucleoli, bound only to the DFC-like core of NLPs while a second mAb that bound to both the DFC and GC of nucleoli, bound to both the core and cortex of NLPs. Thus solubilized components of nucleoli can reassociate in vitro to produce particles that resemble nucleoli in their size, ultrastructure, and protein distribution.

A study on nucleolar DNA: isolation of DNA from fibrillar components and ultrastructural localization of different DNA probes*

The nature and localization of DNA contained in the fibrillar centres and the dense fibrillar component (the fibrillar complex) in the nucleoli, was studied in human LEP cells, Sertoli cells, spermatogonia A and in mitotic chromosomes of stimulated lymphocytes. A novel procedure for isolating the intact fibrillar complex from LEP cells was used; the complex contains DNA that hybridizes to secondary constrictions of mitotic chromosomes and to 28 S rDNA sequences, on Southern blots. Electron microscopic DNA-DNA in situ hybridization was performed, with (a) a probe prepared from DNA extracted from the fibrillar complex of LEP cells, (b) a probe for human total genomic DNA, and (c) a probe for the transcribed part of human rDNA. On the basis of the results obtained we conclude that the ribosomal RNA genes in human Sertoli cells and spermatogonia A are predominantly associated with the dense fibrillar component, including the border region between fibrillar centres and the dense fibrillar component. The ribosomal RNA genes are the main, if not exclusive, DNA type present in the fibrillar complex in the studied cell types.

Mouse rRNA gene transcription factor mUBF requires both HMG-box1 and an acidic tail for nucleolar accumulation: molecular analysis of the nucleolar targeting mechanism.

RNA polymerase I requires at least two nucleolar transcription factors, UBF and SL-1, for ribosomal RNA gene (rDNA) transcription. UBF requires SL-1 for the formation of a stable initiation complex on the rDNA promoter region. We have determined the region of mouse UBF (mUBF) required for nucleolar targeting. Although mUBF has a nuclear localization sequence, this sequence alone is not sufficient for mUBF to accumulate in the nucleolus. Deletion analyses show that mUBF requires a wide region except for the N-terminal 101 amino acids for nucleolar targeting. Deletion of either the HMG-box1, a region crucial for rDNA binding, or the acidic tail, a region that may interact with SL-1, results in the loss of nucleolar targeting. We show by DNA affinity analysis that the HMG-box1 is absolutely necessary for mUBF to bind to the upstream control element of the rDNA. We also show that mUBFs with various internal deletions retain both nucleolar targeting and DNA binding ability. A clear correlation was demonstrated between the DNA binding and nucleolar targeting ability. These results suggest that UBF is transferred to the nucleus by its NLS and is sequestered in the nucleolus by its specific and stable binding to the rDNA promoter via HMG-boxes and the acidic tail.

Immunolocalization of Ku-proteins (p80/p70): Localization of p70 to nucleoli and periphery of both interphase nuclei and metaphase chromosomes

Distribution on both nuclei and metaphase chromosomes of Ku-proteins, recognized by autoantibodies from a patient with systemic lupus erythematosus, has been studied using a specific monoclonal antibody (mAbH6) that recognizes p70, one Ku-protein. Observation with either a conventional fluorescent microscope or a confocal laser scanning microscope revealed mAbH6-stained p70 antigen localized on both nuclear periphery and nucleoli of human interphase cells. The specific staining of nucleoli with mAbH6 has been confirmed using isolated nucleoli from rat liver in which the staining was seen as fine granules surrounding nucleolar DNA. During mitosis p70 antigen moved away from association with the nuclear envelope region to localization on the periphery of condensed chromosomes with no apparent staining of chromosome interior. The p70 antigen was copurified with DNA fragments by immunoaffinity column chromatography using mAbH6. The mAbH6 staining of both nuclear periphery and nucleoli was lost upon digestion with DNase I at low concentrations. These results suggest that p70 antigen is connected with these nuclear structures through DNA.

Nucleolar organizer regions in uterine sarcomas

Nucleolar organizer regions demonstrable by silver staining technique (AgNORs) are loops of nucleolar DNA transcribing to ribosomal RNA. This report quantifies AgNORs in normal endometrium and myometrium, and in leiomyomas and homologous sarcomas of the uterus. The mean AgNOR number in leiomyosarcomas was significantly higher than that in normal myometrium and that in leiomyomas, whereas no significant difference was observed between normal myometrium and leiomyomas. The mean AgNOR count in low-grade endometrial stromal sarcomas was significantly higher than that in normal endometrial stroma, and significantly lower than that in the high-grade variant of the same tumour. The epithelial component of malignant mixed müllerian tumours exhibited a significantly higher mean AgNOR number than normal endometrial epithelium, and the stromal component of these tumours showed a significantly higher mean AgNOR count than normal endometrial stroma and normal myometrium, respectively. The AgNOR count was significantly correlated with the mitotic rate in leiomyosarcomas, in high-grade endometrial stromal sarcomas, and in the epithelial and mesenchymal portions of mixed müllerian tumours, whereas no statistically significant correlation was observed in low-grade endometrial stromal sarcomas. Increased AgNOR counts have been reported for some kinds of malignant tumours in various organs, compared with normal tissues and benign tumours. This study demonstrates a similar increase when homologous uterine sarcomas are compared with histogenetically related normal and neoplastic tissues. AgNOR counting might be a useful adjunct in the classification and grading of uterine tumours.

Determination of the replication time of nucleolar organizer DNA after 5-azacytidine treatment for restricted parts of the S period

In vivo exposure to 5-azacytidine (10−6M) depressed the incorporation of methyl groups to GC rich regions ofAllium cepa L. DNA. Nearly 22% of its 5-methylcytosine residues were under-methylated. The treatment stimulated 1.8 times the rate of [3H]uridine incorporation, as measured in meristems proliferating under steady state kinetics. Nucleologenesis was shortened from 2.7 to 1.6 h in synchronous binucleate cells after 5-azacytidine treatment lasting the whole S period of their previous interphase. By hypomethylating DNA sequences replicated at different times during the S period, it could be inferred that the cistron replication took place in early S. Thus, nucleogenesis was shortened to only 0.6 h after such treatment. Sequential short treatment periods using [3H]thymidine confirmed that the nucleolar organizer regions of the chromosomes replicate in early S.

Fine structural organization of a non-reticulate plant cell nucleus

We studied the fine structural organization of the meristematic nucleus in roots of Lycopesicon esculentum (tomato) using ultracytochemical and immunocytochemical approaches. The nucleus has a non-reticulate (i.e. low DNA content) structure whose supramolecular organization differs in some respects from that in reticulate nuclei, principally in the organization of the chromocentres associated with the nuclear envelope, with which centromeric structures appear to be associated. The main difference at the nucleolar level is found in the fibrillar centres, which have a low amount of DNA labelling and in which inclusions of condensed chromatin are present only very rarely. The distribution of nucleolar DNA amongst the nucleolar compartments is similar to that in reticulate nucleoli as demonstrated using an anti-DNA monoclonal antibody. Tomato nuclei have nucleolus-associated bodies or karyosomes, like other plant species with a low DNA content and non-reticulate nuclear organization. The nuclear ribonucleoprotein structures in the inter- and perichromatin regions, namely inter- and perichromatin fibrils and granules, show similar ultrastructural and cytochemical characteristics in both types of nuclei.

Translocation of dna polymerase-α during the mitotic cycle of Physarum polycephalum

The location of DNA polymerase-α within nuclei of a macroplasmodium of Physarum polycephalum was identified at successive stages of the highly synchronous mitotic cycle by indirect immunofluorescence. The distribution of α-tubulin, the nucleolar protein fibrillarin and DNA were also identified. In G2-phase the polymerase-α was found mainly in the region of the nucleolus. In prophase the polymerase became dispersed into the nucleus with the breakdown of the nucleolus. In metaphase, the polymerase-α was located in two zones separated by the metaphase plate. In S-phase, which follows immediately after mitosis, the distribution of the polymerase was initially punctate but later segments were noted during nucleolar reconstruction. We infer that DNA polymerase-α is stored mainly in the region of the nucleolus (or the reconstructing nucleolus) when it is not needed for DNA replication.

Ultrastructural, cytochemical and immunocytochemical investigation of the interphase nucleus in the unicellular green alga Chlamydomonas reinhardtii

The ultrastructural organization of the interphase nucleus of the green alga Chlamydomonas reinhardtii was investigated and found to be largely dependent on the fixation conditions. In specimens stained with bismuth, densely contrasted granules ranging from 25 to 45 nm in diameter were localized throughout the interchromatin space and often formed clusters. These granules were labeled by RNase A-gold complexes and may represent the counterparts of animal and higher plant cll interchromatin granules. Within the nucleolus the Ag-NOR and pyroantimonate stains and, to a lesser extent, the bismuth stain reacted with the nucleolar dense fibrillar component (DFC). When cells were subjected to a heat shock at 42°C, the nucleolar DFC was found to progressively separate from the nucleolus and, after 3 h, appeared as a continuous meandering thread about 0.1 μm in width. Within the nucleolus, labeling on conventional preparations occurred as small clusters with antibodies to H3 histones or to DNA whereas RNase A-gold complexes labeled most of it including fibrillar centers. Improved ultrastructural preservation in cryofixed, cryosubstituted specimens gently fixed in glutaraldehyde permitted to localize nucleolar DNA predominantly at the outer edge of fibrillar centers and to a lesser extent within the neighbouring DFC. Our results indicate that the structure and composition of Chlamydomonas interphase nuclei are comparable, despite particularities, to those of animal and higher plant nuclei.

A Drosophila anti-rna polymerase ii antibody recognizes a plant nucleolar antigen, rna polymerase i, which is mostly localized in fibrillar centres

The distribution of nucleolar RNA polymerase in the nucleolus of onion root meristematic cells has been studied by means of an antibody originally raised against Drosophila RNA polymerase II. This antibody recognizes the homologous domains of the large subunit of the enzyme, which are highly conserved throughout evolution in the three classes of eucaryotic RNA polymerases. Given that RNA polymerase I is confined to the nucleolus, and that the onion cell nucleolus lacks digitations of extranucleolar chromatin, we conclude that the nucleolar enzyme localized is RNA polymerase I. A quantitative approach, independent of the existence of borderlines between nucleolar fibrillar centres and the dense fibrillar component, allowed us to show that the enzyme is localized in fibrillar centres and in the transition area between them and the dense fibrillar component, in parallel with the nucleolar DNA. These results, together with previous autoradiographic, cytochemical and immunocytochemical results, in this and other species, lead us to conclude that the activation of rDNA for transcription occurs in the fibrillar centres and pre-rRNA synthesis is expressed at the transition area between fibrillar centres and the dense fibrillar component. Fibrillar centres are connected to each other by extended RNA polymerase-bound DNA fibres, presumably active in transcription. This work provides evidence of the high evolutionary conservation of some domains of the large subunit of RNA polymerases and of the existence of fibrillar centres in the nucleolus of plant cells, totally homologous to those described in mammalian cells.

Intranucleolar visualization of nucleic acids and acidic proteins in inhibited and reactivated pea cotyledonary buds

Nuclease-colloidal gold complexes and silver staining were used to visualize intranucleolar nucleic acids and argyrophilic proteins of the nucleolar organizers in bud cotyledonary cells ofPisum sativum. In the G0–1 inhibited bud, a few RNA molecules were detected in the fibrillar component and in the unique fibrillar centre, close to the boundary with the fibrillar component of the nucleolus. DNA was present in the fibrillar component, in the fibrillar centre and in a few fibres crossing the perinucleolar halo. The acidic proteins were localized at the periphery of the fibrillar component but they were also present in the unique fibrillar centre. In the reactivated bud, RNA was particularly concentrated in the granular component and along fibres crossing the perinucleolar halo; a few RNA molecules were also detected at the boundary between the small fibrillar centres and the fibrillar component. DNA was localized in the same nucleolar component as in the inhibited bud, but it was distributed between several fibrillar centres. Acidic proteins coated these DNA loci. In the inhibited and reactivated bud connections between nucleolar DNA containing structures were displayed. The data are discussed in relation to the present knowledge of the functional architecture of the nucleolus.

Nucleolar organizer regions, proliferative activity and DNA index in gastric carcinoma

Nucleolar organizer regions, proliferative activity and DNA index in gastric carcinoma

Timings of DNA synthesis in the nucleoli of Allium cepa L

The timing of nucleolar DNA synthesis has been studied in root tip cells of Allium cepa L. As in animal cells, nucleolar chromatin in this plant species replicates in two phases during S period, once in the early and again towards the end of S phase. Chromatin present in the dense nucleolar component and fibrillar centres, irrespective of being active or inactive, replicates in the early S — phase, whereas the nucleolar associated (hetero) chromatin replicates at the end of S-phase.

Study on mechanism of micronucleoli formation by laser microirradiation

In the male rat kangaroo cell line PTK2, argon laser (514.5 nm) microirradiation of both nucleoli in interphase cells 30, 23, and 12 h before mitosis, and nucleoli in early prophase cells resulted in the formation of micronucleoli, i.e., several small nucleolus-like bodies, in daughter cells. The irradiated cells were stained with methylene blue, which indicated that the nucleolar RNA was destroyed by laser microirradiation. Feulgen staining was applied to the irradiated cells in combination with the measurements of an MPV-II model microphotometer. Irradiated nucleoli were negative for DNA-Feulgen stain, which indicated that nucleolar DNA was destroyed by laser irradiation, so the nucleolar organizer gene was destroyed. After the nucleoli had been irradiated, the cells were continuously incubated at 37 degrees C for 12 and/or 24 h, then fixed and stained with AgNO3. Most of the nucleoli irradiated silver-stained negative that demonstrated that when the nucleoli were irradiated, rDNA was destroyed and transcription stopped. However, some silver grains were found in the nucleoplasm, whereas the nucleoli were silver-stained negative. The results suggest that subsidiary nucleolar organizer loci might exist scattered throughout the genome.

Specific role of manganese and magnesium on RNA synthesis in rabbit bone marrow erythroid cell nuclei

Specific roles of manganese (Mn) and magnesium (Mg) on the activities of DNA-dependent RNA polymerases I and II isolated from rabbit bone marrow erythroid cell nuclei were investigated. Three main polymerases were separated from the cell nuclei. When RNA polymerase I and Mg were added to the RNA synthesis assay mixture containing erythroid cell DNA as template, RNA transcription activity was highest, but when Mg was replaced with Mn, denatured calf thymus DNA formed a better template than erythroid cell DNA. In contrast, nucleoplasmic DNA from erythroid cell and liver DNA were the best templates to stimulate RNA transcription when RNA polymerase II and Mn were added to the assay mixture. However, if Mn was replaced with Mg, RNA synthesis activity was drastically reduced when the template was nucleoplasmic DNA of erythroid cell. RNA polymerase I and Mg synthesized GC rich RNA, whereas RNA polymerase II and Mn synthesized AU rich RNA. Sedimentation analysis showed that the molecular weights of the RNA produced by polymerase I were larger when the enzyme was activated with Mg than with Mn, whereas those of the RNA produced by polymerase II were larger with Mn than with Mg. Furthermore, RNA produced by polymerase I and Mg using chromatin as a template hybridized better with nucleolar DNA than with nucleoplasmic DNA, whereas that produced by polymerase II and Mn hybridized better with nucleoplasmic DNA than with nucleolar DNA. These results suggest that RNA synthesis is dependent on the activity of specific RNA polymerases and the presence of specific divalent cations and templates, and that the cofactor and template for RNA polymerase I are, respectively, Mg and the nucleolar DNA of cell nuclei, whereas those for RNA polymerase II are Mn and nucleoplasmic DNA.

Correlation studies between the binding of aflatoxin B1 to chromatin components and the inhibition of RNA synthesis

Aflatoxin B1 (AFB1) is a potent inhibitor of rat liver nuclear and nucleolar RNA synthesis. However, since after activation AFB1 binds to both DNA and chromosomal proteins, the question is which form of binding is responsible for the inhibition of RNA synthesis. Male Sprague-Dawley rats (200 g) were given i.p. injections of 10, 50, 100, 300 and 500 micrograms AFB1 per 100 g body wt containing 50 microCi [3H]AFB1 (sp. act. 25 Ci/mmol), and the animals sacrificed 2 h later. Liver nuclei, nucleoli and P-3 (a transcriptionally active subnucleolar fraction that is 3.4-fold enriched in active rDNA) were isolated and the binding of AFB1 to DNA and protein of each fraction was determined by DNase I digestion and 5% trichloracetic acid (TCA) hydrolysis. We found that the binding of AFB1 to both nuclear and nucleolar DNA plateaus at 300 micrograms AFB1 per 100 g body wt with values around 100 and 400 pmol AFB1 per mg nuclear and nucleolar DNA, respectively. On the other hand, the binding to protein is linear, although with different slopes, for both nuclear and nucleolar fractions even at 500 micrograms AFB1 per 100 g body wt, the highest dose used. Since AFB1 inhibition of nuclear and nucleolar RNA synthesis plateaus respectively at 60% and 90% inhibition levels at the dose of 300 micrograms AFB1 per 100 g body wt, these results suggest the binding of AFB1 to DNA, but not to protein, is responsible for the inhibition of RNA synthesis. Further support for this contention is obtained by comparing the binding and the inhibition data between P-3 and nucleoli. P-3 is three times more transcriptionally active than nucleoli and, as a result, is more sensitive to AFB1 inhibition. This greater sensitivity is reflected by the specific binding activity of AFB1 to P-3 DNA, which is greater than 50% higher than to nucleolar DNA. In contrast, this effect is not reflected by the specific binding activity of AFB1 to protein which is exactly the same for both fractions.

Cell cycle parameters of adult rat hepatocytes in a defined medium. A note on the timing of nucleolar DNA replication.

Hepatocytes, isolated from adult (250-350 g) rats, attached and survived well in primary culture on highly diluted (less than 1 microgram/cm2) collagen gel in a synthetic medium without serum or hormones. About 20% of the cells "spontaneously" entered S phase during the first 4 days of culturing, and mitoses were easily demonstrated at the near physiological concentration (1.25 mM) of Ca++ prevailing in the medium. Cultures given 9 nM epidermal growth factor (EGF) and 20 nM insulin 20 h after inoculation showed vigorous DNA synthesis and mitotic activity. Autoradiography of such cells exposed to [3H]thymidine allowed the determination of the following cell cycle parameters: Lag period from EGF/insulin stimulation till onset of increased DNA synthesis, 17 h; rate of entry into S phase (kG1/S), 0.028/h; duration of S phase, 8.4 h; duration of G2 phase, 2.7 h. The peak DNA synthesis (pulse labelling index, 24%) and peak mitotic activity (mitotic index, 1.7%) occurred 35 and 43 h, respectively, after the stimulation with EGF/insulin. These values are comparable to those reported during the in vivo compensatory hyperplasia following partial hepatectomy of adult rats. A marked variation of the intranuclear [3H]thymidine pulse labelling pattern was noted: During the first 1.5 h of the S phase, the labelling was extranucleolar and during the last 1.5 h chiefly nucleolar. The cells survived well in the absence of glucocorticoid, whose effect on cell cycle parameters therefore could be studied. Dexamethasone (25-250 nM) did not appreciably affect the durations of S phase and G2 phase or the pattern of preferential extranucleolar and nucleolar DNA synthesis within the S phase.

Human U3 small nucleolar RNA genes are localized to the nucleoplasm

U3 RNA, an abundant, conserved, capped, small RNA localized to the nucleolar compartment of eukaryotic cells, is implicated in the processing of pre-ribosomal RNA. The genes for U1 and U2 snRNAs ( s mall n uclear RNAs) are clustered and present in the nucleoplasmic DNA; however, the localization of U3 snRNA genes is not known. DNAs, isolated from HeLa cell nuclei and nucleoli, were hybridized with labeled probes corresponding to 1) the 5′-flanking and 2) the coding regions of the human U3 snRNA gene. The intensity of signals obtained with both the probes were 5–6 fold greater in nuclear DNA, compared to nucleolar DNA. With ribosomal gene probe, the nucleolar DNA had sixfold more intense signal than nuclear DNA. These results indicate that genes for U3 snRNA are in the nucleoplasm. Therefore, U3 snRNA, like 5S ribosomal RNA, appears to be synthesized in the nucleoplasm and transported to the nucleolus.