Ultrastructural distribution of DNA and RNA within the nucleolus of human Sertoli cells as seen by molecular immunocytochemistry

Ribosome biogenesis: from structure to dynamics

In this chapter we describe the status of the research concerning the nucleolus, the major nuclear body. The nucleolus has been recognized as a dynamic organelle with many more functions than one could imagine. In fact, in addition to its fundamental role in the biogenesis of preribosomes, the nucleolus takes part in many other cellular processes and functions, such as the cell-cycle control and the p53 pathway: the direct or indirect involvement of the nucleolus in these various processes makes it sensitive to their alteration. Moreover, it is worth noting that the different nucleolar factors participating to independent mechanisms show different dynamics of association/disassociation with the nucleolar body.

HRad17 colocalizes with NHP2L1 in the nucleolus and redistributes after UV irradiation

The rad17 gene of Schizosaccharomyces pombe plays an important role as a checkpoint protein following DNA damage and during DNA replication. The human homologue of S. pombe rad17, Hrad17, was recently identified, but its function has not yet been established. Using the yeast two-hybrid system, we determined that HRad17 can interact with a nucleolar protein, NHP2L1. This interaction was also demonstrated biochemically, in human cells. Immunofluorescence studies revealed that HRad17 and NHP2L1 colocalize to the nucleolus, and immunogold labeling further resolved the location of NHP2L1 to the dense fibrillar component of the nucleolus. Interestingly, the localization of HRad17 in the nucleolus was altered in response to UV irradiation. These results provide some insight into the DNA damage and replication checkpoint mechanisms of HRad17.

Ultrastructural methods for nucleic acid detection by immunocytology

In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.

Nucleolar substructures of rabbit cleaving embryos: an immunocytochemical study

The structure-function relationships of the nucleolar substructures were studied in preimplantation rabbit embryos, where nucleologenesis is extending over the first four cell cycles and may not be synchronous in each blastomere. Immunocytochemical methods using light and electron microscopy were applied for protein and RNA localization as well as nick translation and terminal deoxynucleotidyl transferase techniques for DNA detection. DNA was gradually associated with the periphery of the compact nucleolar precursor bodies (NPBs) but was never found inside NPBs at the four-cell stage. In 16-cell embryos, some NPBs displayed a reticulated periphery forming the branching network of the dense fibrillar component (DFC) surrounding the "residual body" (remnant of NPB) in the process of activation. At the 32-cell stage, fully reticulated nucleoli were observed in each blastomere. DNA was then associated with the DFC of reticulated nucleoli. RNA was first detected at the 16 cell-stage in close contact with the DFC as well as inside the "residual body" which was not immunolabeled with the DNA antibodies used. When observed by light microscopy, fibrillarin, nucleolin, and protein B23 displayed a changing distribution pattern during nucleologenesis. At early stages (up to the 16-cell stage), small dot- and spot-like structures were distributed within the whole nuclei. In 16-cell embryos, these proteins started to accumulate in an irregular thin layer around the NPBs in the process of activation. The reorganization process described may be in relation with the redistribution of chromatin and nuclear/nucleolar matrix components during the activation of rDNA transcription localized in the NPB shell. In conclusion, nucleologenesis is only achieved at the fourth cell cycle in the cleaving rabbit embryo at the corresponding time when the first detectable nucleolus-associated RNA is detectable. Our results show a good correlation between the establishment of structure and function.

Analysis of nucleolar transcription and processing domains and pre-rRNA movements by in situ hybridization

We have examined the cytological localization of rRNA synthesis, transport, and processing events within the mammalian cell nucleolus by double-label fluorescent in situ hybridization analysis using probes for small selected segments of pre-rRNA, which have known half-lives. In particular, a probe for an extremely short-lived 5' region that is not found separate of the pre-rRNA identifies nascent transcripts within the nucleolus of an intact active cell, while other characterized probes identify molecules at different stages in the rRNA processing pathway. Through these studies, visualized by confocal and normal light microscopy, we (1) confirm that rDNA transcription occurs in small foci within nucleoli, (2) show that the nascent pre-rRNA transcripts and most likely also the rDNA templates are surprisingly extended in the nucleolus, (3) provide evidence that the 5' end of the nascent rRNA transcript moves more rapidly away from the template DNA than does the 3' end of the newly released transcript, and (4) demonstrate that the various subsequent rRNA processing steps occur sequentially further from the transcription site, with each early processing event taking place in a distinct nucleolar subdomain. These last three points are contrary to the generally accepted paradigms of nucleolar organization and function. Our findings also imply that the nucleolus is considerably more complex than the conventional view, inferred from electron micrographs, of only three kinds of regions - fibrillar centers, dense fibrillar components, and granular components - for the dense fibrillar component evidently consists of several functionally distinct sub-domains that correlate with different steps of ribosome biogenesis.

The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus

The nucleus is an intricately structured integration of many functional domains whose complex spatial organization is maintained by a nonchromatin scaffolding, the nuclear matrix. We report here a method for preparing the nuclear matrix with improved preservation of ultrastructure. After the removal of soluble proteins, the structures of the nucleus were extensively cross-linked with formaldehyde. Surprisingly, the chromatin could be efficiently removed by DNase I digestion leaving a well preserved nuclear matrix. The nuclear matrix uncovered by this procedure consisted of highly structured fibers, connected to the nuclear lamina and built on an underlying network of branched 10-nm core filaments. The relative ease with which chromatin and the nuclear matrix could be separated despite extensive prior cross-linking suggests that there are few attachment points between the two structures other than the connections at the bases of chromatin loops. This is an important clue for understanding chromatin organization in the nucleus.

Structural changes in oocyte nucleoli of Xenopus laevis during oogenesis and meiotic maturation

Immunoelectron microscopy with anti-nucleolin defined substructures within the multiple nucleoli of biosynthetically active stage II-III oocytes and within the nucleoli of relatively quiescent stage VI oocytes of Xenopus laevis. Dense fibrillar components (DFCs) of nucleoli from stage II-III oocytes consisted of nucleolonemas that radiated from a continuous DFC sheath surrounding fibrillar centers (FCs). Discernible granular regions (GRs) were absent in these same nucleoli. Conversely, stage VI oocyte nucleoli displayed compacted DFCs and prominent GRs. Immunofluorescence microscopy then tracked fibrillarin, nucleolin, and condensed DNA through oogenesis and into progesterone-induced meiotic maturation and nuclear breakdown. In stage II-III oocyte nucleoli, fibrillarin was enriched near the FC-DFC boundaries, while nucleolin was distributed throughout these same DFCs. Both proteins were enriched within the compacted DFCs of stage VI oocyte nucleoli. Staining with (DAPI) 4',6-diamidino-2-phenylindole showed condensed DNA within nucleolar FCs of both stage II-III and stage VI oocyte. Upon nuclear breakdown, we found fibrillarin and nucleolin in small particles and in the surrounding cytoplasm. Although we saw no trace of fibrillarin or nucleolin in nuclear remnants prepared just minutes later, DAPI-stained particles remained within these preparations, thus suggesting that FCs were at least slow to disassemble.

Multiparameter microscopic analysis of nucleolar structure and ribosomal gene transcription

A survey of novel microscopic approaches for structural and functional analysis of subnucleolar compartments will be presented. Research on nucleolar structure and function concentrates predominantly on two distinct types of nucleoli: (1) nucleoli present during the interphase of the cell cycle in somatic tissue culture cells and (2) nucleoli present in meiotic cells, e.g. oocytes of amphibians. These nucleoli are found during meiotic prophase of oogenesis and are functional during several months of the diplotene stage of oogenesis. A further characteristic is the fact that these nucleoli are extrachromosomal, since they originate by selective ribosomal DNA (rDNA) amplification during the early pachytene stage of oogenesis. Miller-type chromatin spread preparations using transcriptionally active nucleoli, to a major part, contributed to our understanding of the structural organization of polymerase I directed pre-rRNA transcription. Although the structural organization of the template-associated pre-rRNA transcript is known in some detail from chromatin spreads, relatively little is known about structural aspects of pre-rRNA processing. In order to investigate this intriguing question in more detail, we have developed a computer-based densitometry analysis of both template-associated and template-dissociated pre-rRNA transcripts in order to follow the structural modification of pre-rRNA transcripts during processing. Another line of experiments is devoted to the in situ structure of actively transcribing genes in the nucleolus. In order to bridge the gap between light microscopy and electron microscopy we started video-enhanced light microscopical analysis of actively transcribing genes. Although the dimensions of individual spread genes are critical for detection by optical microscopy, we succeeded in obtaining the first series of images of transcribing genes in their "native' hydrated state. An additional promising type of microscopy is transmission X-ray microscopy. Recent progress in instrumentation as well as in sample preparation has allowed us to obtain the first images of density distribution within intact, fully hydrated nucleoli using amplitude-contrast and/or phase-contrast X-ray microscopy of non-contrasted, fully hydrated nucleoli at different states of transcriptional activity. Whereas the above mentioned investigations using video microscopy and X-ray microscopy are predominantly applicable to the analysis of amplified nucleoli in amphibian oocytes, which are characterized by an extremely high transcription rate of 80-90% of rDNA genes per individual nucleolus, structural analysis of the in situ arrangement of actively transcribing genes in somatic nucleoli as present in the interphase nucleus is far more difficult to perform, mainly due to the much lower number of simultaneously transcribed active genes per individual nucleolus. Visualization of actively transcribed gene clusters is approached by an integrated experimental assay using video microscopy, confocal laser scan microscopy, and antibodies against specific nucleolar proteins.

rRNA distribution during microspore development in anthers of Beta vulgaris L. quantitative in situ hybridization analysis

We related changes in the ultrastructural organization of the nucleoli with the results of quantitative in situ hybridizations to characterize rRNA metabolism during the development of microspore mother cells in the sugar beet anther (Beta vulgaris L.). In the course of meiotic prophase and early postmeiotic interphase the morphological characteristics of the nucleoli are typical of low or no transcriptional activity and a low rate of rRNA processing. However, we found evidence of an apparent increase in the relative numbers of 18 S rRNA transcripts in some stages of microsporogenesis. This was found in both the nucleoli and cytoplasm of pachytene meiocytes, and in later stages there was a spectacular accumulation of rRNA transcripts in nucleoli of the tetrad cells. Quantitative data are analyzed in the light of morphometric findings in the cell and their compartments to elucidate the degree to which changes in cell size are related to changes in labeling density and distribution. The results are discussed in terms of rRNA synthesis, transport and degradation as processes involved in the regulation of rRNA within microsporocytes and microspores.

Intranuclear retention of ribosomal RNAs in response to herpes simplex virus type 1 infection

The localization of ribosomal RNA (rRNA) was investigated at the ultrastructural level in herpes simplex virus type 1 infected HeLa cells using three distinct biotinylated probes which bind in sequence to three different segments of the ribosomal genes. Comparison of the above with the signal levels obtained from non-infected cells reveals information about the effects of HSV-1 infection on ribosome biogenesis. A probe specific for the 5′ end portion of pre-rRNA labeled all nucleoli of both non-infected and infected cells in the same way, that is, it mainly labeled the dense fibrillar component and the border of the fibrillar centers but only slightly labeled the granular component. This indicates that the initial cleavage of pre-rRNA in herpes infection still occurs in the 5′ region of the 5′ external transcribed spacer. However, a probe specific for 18 S rRNA labeled the granular component of the nucleoli more intensely after infection. In addition, significant amounts of rRNA molecules were present within the intranuclear viral region, except over the enclosed viral dense bodies, and within the virus-enlarged clusters of interchromatin granules. The data indicate that the still enigmatic viral dense bodies, which are nucleolus-related structures, are excluded from the marked intranuclear retention of ribosomal RNAs and, in addition, reveal a possible role for the interchromatin granules of infected cells in the regulation of the export of the ribosomal subunits towards the cytoplasm.

Robert Feulgen Prize Lecture 1995. New approaches to in situ detection of nucleic acids

The present paper reviews recent results obtained by different molecular biology-based, immunocytological approaches to the localization and identification of nucleic acids in sections of biological material. Examples of sensitive, high-resolution detection methods for RNA, DNA or specialized DNA regions are presented. Special emphasis is placed on the potential values and limitations of these new methods.

Subnucleolar location of fibrillarin and variation in its levels during the cell cycle and during differentiation of plant cells

The nucleolar protein fibrillarin has been studied in onion cells; it is detected as an M(r) 37,000 protein by immunoblotting using a human autoimmune serum. Quantitative immunoelectron microscopy showed that most fibrillarin is localized in the transition zone between the fibrillar center (FC) and the dense fibrillar component (DFC) as well as in the proximal zone of the DFC, where the labeling shows a gradual decrease outward until it reaches insignificant levels in the distal zone of the DFC. Thus, fibrillarin is not uniformly distributed throughout the DFC of plant cells. This result supports the hypothesis that the morphologically homogeneous DFC may not be uniform in function; it is also in agreement with the hypothesized vectorial flow of ribosome biogenesis through the same compartments. Data are also presented showing that the amount of fibrillarin increases when nucleolar activity increases in G2, and probably decreases when nucleolar activity decreases during differentiation.

Nucleic acid compartmentalization within the cell nucleus by in situ transferase-immunogold techniques

In the present review, we report on recent results obtained by in situ transferase-immunogold techniques as to the ultrastructural distribution of DNA and RNA within the cell nucleus. Special emphasis is placed on the various nucleolar components and the various enigmatic structures of the extranucleolar region: interchromatin granules, coiled bodies, and simple nuclear bodies. These data are discussed in the light of our current understanding of the functional organization of the cell nucleus.

Localization of fibrillarin and nucleolin in nucleoli of mouse preimplantation embryos

The localization of fibrillarin and nucleolin in the nuclei of mouse two-cell, four-cell, and eight-cell embryos has been studied using immunofluorescent staining with specific antibodies. In all of these cleavage stages, both antigens were associated exclusively with the peripheral region of the nucleolus precursor bodies (NPBs). The original speckled fluorescent staining pattern in the early two-cell stage was progressively changed into a continuous fluorescent-positive layer localized in the cortex of the NPBs in the four-cell embryos. The compact central area of NPBs was never stained. Both proteins were colocalized in the same substructures of developing nucleoli. In order to analyze the interaction of chromatin with NPBs, DNA structures were specifically immunolabelled. At the time of resumption of nucleolar transcription (in the two-cell mouse embryo), DNA was detected at the periphery of, but not penetrating into, NPBs. Our results confirm the view that the cortical region of NPBs could represent a nucleolonemal area involved in the resumption of nucleolar transcription in the early mouse embryo.

Nuclear phospholipids during the adaptation of human EUE cells to hypertonic stress

The phospholipid component of interphase nuclei was analysed in EUE cells (an established cell line from embryonic human epithelium) grown in an isotonic culture medium and during the adaptation process to a hypertonic medium, using a highly specific ultracytochemical procedure, viz. labelling with the phospholipase A2 gold-complex. Within the nucleus, the phospholipids were localized in domains involved in different steps of the synthesis and processing of the RNA. These localizations did not vary at the two key steps of the adaptation process to hypertonic medium: short-term treatment (6 h) representing critical shock condition, and long-term growth (5 days) representing the adapted cells under survival conditions. On the contrary, deep changes of the labelling intensity of phospholipids at these sites occurred at the different times of hypertonic treatment and followed the same course as those observed in the ultramorphological patterns of transcription: the chromatin condensation, as evaluated by image analysis, the permanent nucleolar components, the interchromatin and the perichromatin granules. These data endorse the hypothesis that nuclear phospholipids could be involved in different steps of the transcriptional activity. They are indicative of the deep changes occurring in the EUE cells submitted to hypertonic stress.

The comparative cell biology of accessory somatic (or Sertoli) cells in the animal testis

A comparative account is given of recent advances in the cell biology of testicular accessory somatic (or Sertoli) cells in mammals, nonmammalian vertebrates, and invertebrates by comparing and contrasting their structure and function. Their structure is discussed in relation to the nucleus, cytoplasmic organelles, and inclusions (lipids, the cytoskeleton, junctional complexes, and blood-testis barrier, which show great diversity and a variable testicular architecture), and mode of spermatogenesis. A very limited somatic cell-germinal association or its complete absence is observed in some groups of invertebrates. Wherever the somatic accessory cells are present, their comparative functions are discussed in relation to (1) mechanical support and nutrition; (2) translocation of germ cells; (3) paracrine regulation and a combination of male germ cell proliferation and differentiation by secretion of regulatory proteins, including peptide growth factors and hormones; (4) phagocytosis; (5) steroid hormone synthesis and metabolism; and (6) spermiation. Comparative cellular and molecular aspects of Sertoli cell-germ cell and peritubular cell interactions and the regulatory (hormonal) mechanisms involved as well as gaps in our knowledge about the molecular aspects of these interactions are emphasized for a better understanding of diversity in the patterns and regulation of spermatogenesis in animals.

Cytochemical and immunocytochemical study of coiled bodies in different cultured cell lines

We analyzed by different cytochemical and immunocytochemical approaches the biochemical compositon of coiled bodies in three different cultured cell lines. Coiled bodies are stained by the AgNOR staining method and by the EDTA regressive staining method preferential for ribonucleoprotein (RNP). Using the in situ polyadenylate nucleotidyl transferase-immunogold technique or anti-RNA antibodies, we decisively demonstrated the presence of appreciable amounts of RNA in coiled bodies. Neither the in situ terminal deoxynucleotidyl transferase-immunogold technique nor anti-DNA antibodies revealed any DNA in coiled bodies. Coiled bodies thus appear as distinct regions of cell nuclei involved in some steps of RNA metabolism but not directly in RNA synthesis. Their relationships with the dense fibrillar component of the nucleolus and with interchromatin granule clusters are discussed.

The nucleolus

The transcriptionally active rRNA genes have the remarkable ability to organize and integrate the biochemical pathway of ribosome production into a structural framework, the nucleolus. The past year has seen numerous advances in our understanding of the relationships between nucleolar substructures, the site of ribosomal RNA (rRNA) gene transcription and the pathway of ribosome maturation. Progress has also been made both in the molecular identification of nucleolar constituents and in our understanding of the interactions between these components and their assembly into higher order structures.

Ultrastructural rRNA localization in plant cell nucleoli. RNA/RNA in situ hybridization, autoradiography and cytochemistry

The distribution of ribosomal transcripts in the plant nucleolus has been studied by non-isotopic in situ hybridization in ultrathin Lowicryl K4M sections and by high-resolution autoradiography after labelling with tritiated uridine. In parallel, cytochemical techniques were applied to localize RNA on different plant nucleolar components of Allium cepa L. root meristematic cells and Capsicum annuum L. pollen grains. For RNA/RNA in situ hybridization, several biotinylated single-stranded ribosomal RNA probes were used for mapping different fragments of the 18 S and the 25 S rRNA gene transcribed regions. Ribosomal RNAs (from pre-rRNAs to mature 18 and 25 S RNAs) were found in the nucleolus, in the dense fibrillar (DFC) and granular components (GC). Hybridization signal was found at the periphery of some fibrillar centres (FCs) with probes recognizing both 18 and 25 S rRNA sequences. A quantitative study was performed to analyze the significance of this labelling. Incorporation of tritiated uridine into roots was carried out and, later, after a long time-exposure, autoradiography revealed the presence of newly synthesized RNA mainly in the DFC and at the periphery of the FCs. The presence of RNA in these areas was also confirmed by the cytochemical techniques used in this study. Taken together, these data favour the hypothesis that transcription can begin at the periphery of the FCs, although we cannot exclude the possibility that the DFC plays a role in this process.