Widely dispersed DNA within plant and animal nucleoli visualised by 3-D fluorescence microscopy

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 three-dimensional organization of ribosomal genes and the architecture of the nucleoli vary with G1, S and G2 phases

The three-dimensional (3-D) organization of the nucleolus, a defined nuclear territory containing tandem repeats of the ribosomal genes (rDNA), was investigated in PtK1 cells. Identification of the interphase stages was performed in single cells using DNA quantification by cytometry for the G1 and G2 phases while the S phase was identified by immunolabelling of the proliferating cell nuclear antigen (PCNA). The 3-D organization of the rDNA in the nucleolus was analyzed by fluorescence in situ hybridization using confocal microscopy. All the rDNA was located inside the nucleolar structures during all stages and the two rDNA loci were orthogonal. The rDNA was heterogeneously distributed in each nucleolus during G1, S and G2, with alternate sites of clustered genes (spots) and of genes in more extended configurations. The number of spots (4 to 6 in G1) increased during S phase (7 to 12) and their 3-D organization was progressively relaxed from G1 to G2. Double spots in G2 could reflect a similar gene organization of two chromatids. During mid-S phase, PCNA co-localized with some clustered genes (spots), indicating that rDNA replication occurs inside nucleoli and at different sites of the same locus simultaneously. The evaluation of the rDNA transcription units in 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)-treated cells indicated a mean of 16 units per G1 nucleus and 25 units per G2 nucleus. For G1 and G2, the fine 3-D structure of nucleoli was reconstructed using ultrathin serial sections after specific contrast of DNA and RNA, digitization of the serial section images and computer-assisted 3-D architecture. Fibrillar centers (FCs) formed discrete structures (about 10 in G1 and 20 in G2) connected by a network of the dense fibrillar component. The 3-D arrangement of the FCs in G1 and G2 are similar to the rDNA spots. In conclusion, the architecture of the nucleoli during interphase reflects the distribution of the rDNA that is characterized by alternation of clustered and extended genes.

Cytochemistry and immunocytochemistry of nucleolar chromatin in plants

This review attempts to document the most relevant data currently available on the in situ localization of nucleolar chromatin on plant cells. The data provided by the most powerful and recent in situ techniques, such as DNA specific ultrastructural staining, immunogold labelling, in situ molecular cytochemistry, in situ hybridization or confocal microscopy, are summarized and discussed in the light of the potential and limitations of each individual methodology. The presence of DNA in both fibrillar centres and regions of the dense fibrillar component is extensively documented. Data on the nucleolar distribution of other important macromolecules involved in ribosomal transcription are also shown and referred to with regard to the location of DNA. The comparison with the available data on the animal cell nucleolus points towards models of similar functional organization in both plant and animal nucleoli.

Nuclear Fos domains in transcriptionally activated supraoptic nucleus neurons

This study has analysed by light and electron microscopy immunolocalization the nuclear pattern of distribution of Fos-related proteins in supraotic neurons. Two experimental models of transcriptional activation have been used: sustained, global transcriptional activation, at relatively near physiological conditions, by six days of chronic intermittent salt loading; and superinduction of c-fos gene by this salt loading regime plus cycloheximide treatment for 4 h. In the first condition, the ultrastructural analysis showed a distribution of Fos-like immunoreactivity on the reticular network of dispersed chromatin that extends between the nucleolar surface and the nuclear envelope, whereas the Fos-negative adjacent interchromatin spaces appeared rich in interchromatin granules by using a cytochemical staining for ribonucleoproteins. The nucleolus associated heterochromatin, fibrillar centers of the nucleolus and coiled bodies were free of immunoreactivity. This immunoelectron pattern seems to indicate that active genes containing activator protein-1 and cyclic AMP response element recognition sites are extensively distributed in euchromatin regions and suggests that the Fos-positive nuclear domains correspond to the actively transcribing chromatin regions, at least in supraoptic neurons. It also suggests that these Fos-positive transcription domains are complementary to adjacent ribonucleoprotein-rich interchromatin spaces which are involved in the processing and splicing of pre-messenger RNA. Moreover, the absence of immunoreactivity on the fibrillar centers, the sites of pre-ribosomal RNA synthesis, suggests that the Fos protein complexes are not involved in regulating the expression of ribosomal RNA genes. Following superinduction of c-fos gene by osmotic stimulation plus cycloheximide treatment, a conspicuous Fos-like immunoreactivity was detected in dispersed chromatin regions, whereas the heterochromatin masses, nucleoli and coiled bodies showed no immunoreaction. Moreover, this treatment induced the formation of nuclear "dense bodies" of a fibrillar nature which were free of immunolabelling. Since Fos proteins are known to be short-lived, the expression of these nuclear constituents, under conditions of protein synthesis inhibition induced by the cycloheximide, suggests the stabilization of chromatin-bound Fos complexes or, alternatively, a preferential synthesis of Fos proteins.

Different patterns of rDNA distribution in Pisum sativum nucleoli correlate with different levels of nucleolar activity

We have used in situ hybridization with probes to rDNA, labelled either with digoxygenin or directly with fluorescein, to determine the arrangement of these genes within the nucleoli of Pisum sativum L. root cells. Confocal laser scanning microscopy was used to image the three-dimensional structures revealed, but we have also compared this technique with deconvolution of conventional (wide-field) fluorescence images measured with a cooled CCD camera, and have shown that the results are remarkably similar. When the deconvolution technique was applied to the confocal data it gave clearer images than could be achieved by confocal microscopy alone. We have analysed the distribution of rDNA in the different cell types observable in root tips: the quiescent centre; active meristematic cells; and relatively differentiated root cap, epidermal and cortical cells. In addition to four perinucleolar knobs of condensed, inactive rDNA genes, corresponding to the four nucleolar organizers in P. sativum, which were the most brightly labelled structures, several characteristic patterns of intranucleolar labelling were apparent, including bright foci, large central chromatin masses, and fine, decondensed interconnecting fibres. The larger and more active the nucleolus, the smaller the proportion of condensed perinucleolar rDNA. In some large and active meristematic nucleoli, all the internal rDNA is decondensed, showing that transcription cannot be restricted to the bright foci, and is most likely to occur on the decondensed fibres.