Quantitative analysis of rat liver nucleolar and nucleoplasmic ribosomal ribonucleic acids

New Chromatin Run-On Reaction Enables Global Mapping of Active RNA Polymerase Locations in an Enrichment-free Manner

The development of a simple and cost-effective method to map the distribution of RNA polymerase II (RNPII) genome-wide at a high resolution is highly beneficial to study cellular transcriptional activity. Here we report a mutation-based and enrichment-free global chromatin run-on sequencing (mGRO-seq) technique to locate active RNPII sites genome-wide at near-base resolution. An adenosine triphosphate (ATP) analog named N⁶-allyladenosine triphosphate (a⁶ATP) was designed and could be incorporated into nascent RNAs at RNPII-located positions during a chromatin run-on reaction. By treatment of the run-on RNAs with a mild iodination reaction and subjection of the products to reverse transcription into complementary DNA (cDNA), base mismatch occurs at the original a⁶A incorporation sites, thus making the RNPII locations detected in the high-throughput cDNA sequencing. The mGRO-seq yields both the map of RNPII sites and the chromatin RNA abundance and holds great promise for the study of single-cell transcriptional activity.

Key role of the achievement of an appropriate ribosomal RNA complement for G1-S phase transition in H4-II-E-C3 rat hepatoma cells

Cell growth is closely related to cell proliferation and an adequate ribosome biogenesis appears to be necessary for cell duplication. In the present study, we have investigated the relationship between rRNA synthesis and cell cycle progression. For this purpose, in a first set of experiments, we evaluated the effect of rRNA synthesis variation on cycle duration in asynchronously growing H4-II-E-C3 rat hepatoma cells. Cells were either treated with insulin or insulin plus actinomycin D (AMD). The hormone stimulated ribosome biogenesis, which was later followed by an increased synthesis of DNA and a shortening of cell doubling time (DT). Bivariate flow cytometry indicated that the reduced length of the cell cycle was mainly due to the shorter G1-phase. AMD, at the concentration of 0.04 microg/ml, hindered ribosome biogenesis without affecting heterogeneous RNA production. A 12-h reduction in ribosome biogenesis level by AMD caused a lowering of DNA synthesis and a lengthening of cell DT with a longer G1-phase. In a second set of experiments, we analyzed the cell content variations of 28S and 18S rRNA transcripts during G1 phase in H4-II-E-C3 cells, synchronized by serum deprivation, and then stimulated by serum, serum plus insulin, and serum plus insulin and AMD. In control cells, a progressive increase in rRNA content occurred until the highest value of rRNA content was reached 21 h after serum stimulation. In insulin-treated cells, the highest rRNA value was reached at 12 h whereas in AMD-treated cells, the rRNA quantity was constantly low until 18 h and then sharply increased at 21 h. In the three experimental conditions, the highest values of rRNA amount were reached at the end of G1 phase and were quite similar to one another. We also evaluated, by real-time RT-PCR, cyclin E mRNA expression, which appeared to sharply increase at those times in which the maximum increase in the rRNA content was observed. Our results indicated that the achievement of an appropriate amount of rRNA allows G1/S phase transition, probably by modulating the expression of cyclin E mRNA.

Increased mortality rate and not impaired ribosomal biogenesis is responsible for proliferative defect in dyskeratosis congenita cell lines

X-linked dyskeratosis congenita is a rare inherited disorder mainly characterized by progressive changes in proliferating epidermal, mucosal, and bone marrow tissues that commonly emerge after 10 y of life. It is caused by mutations of the DKC1 gene, which codes for dyskerin, a protein that may play a role in ribosomal biogenesis. In order to verify whether the defects of proliferating tissues observed in dyskeratosis congenita are due to an altered ribosome synthesis, we studied ribosomal biogenesis in relation to cell proliferation in two lymphoblastoid cell lines from dyskeratosis congenita patients and in one control line. We observed that in the dyskeratosis congenita cell lines the rRNA transcription and maturation and proliferative capability remained unimpaired. Increasing the number of cell cycles, however, leads to a steep rise in the apoptotic fraction of dyskeratosis congenita cells, which is not observed in controls. These findings demonstrate that whereas dyskeratosis congenita cell lines do not display proliferation defects, they do show progressively increasing levels of apoptosis in relation to the number of cell divisions. This concept is consistent with (i) the delayed onset of dyskeratosis congenita proliferating-tissue defects, which do not emerge during embrional development as would be expected with ribosomal biogenesis alterations, and (ii) with the increasing severity of the proliferating-tissue defects over time.

Transcription of ribosomal DNA intergenic spacer sequences in normal and regenerating rat liver

In regenerating rat liver both the transcriptional activity of the intergenic spacer rDNA promoter and the steady-state abundance of spacer transcripts are increased about 2-fold, as compared to normal liver. These changes are parallel to the observed 2.5-fold increase in regenerating liver of rRNA gene promotor activity and gene promotor transcripts abundance. These results suggest that both gene and spacer rDNA promotors are subject to common regulatory mechanisms. Our results indicate also that the stability of spacer transcripts in regenerating liver is not significantly altered.

The Ag-NOR proteins and transcription and duplication of ribosomal genes in mammalian cell nucleoli

The relationship between the Ag-NOR (silver-stained Nucleolar Organizer Region) proteins and the functional-structural organization of the nucleolar ribosomal chromatin was studied in regenerating and cortisol-stimulated rat hepatocytes. Statistical analysis of Ag-NOR proteins, carried out with an automated image analyzer, indicated that in regenerating rat hepatocytes the quantity of Ag-NOR proteins mainly increased between the 4th and 12th h of regeneration, reaching a level twice that of resting hepatocytes. Also the synthesis of pre-ribosomal RNA (pre-rRNA) was stimulated after the 4th h of regeneration. Cycloheximide administered to rats at a dose of 0.025 mg/100 g body weight (bw) prevented any increase in Ag-NOR proteins but did not hinder the stimulation of pre-rRNA synthesis. In 8 h cortisol-stimulated hepatocytes no significant change in amount of Ag-NOR protein was observed whereas pre-rRNA synthesis was highly increased as in 12 h regenerating hepatocytes. These results indicated that in rat hepatocytes Ag-NOR proteins and stimulation of pre-rRNA synthesis are not related. The relationship between the Ag-NOR proteins and the distribution of the completely extended intranucleolar ribosomal chromatin was also studied in regenerating rat hepatocytes. At 12 h after partial hepatectomy an increased amount of completely extended ribosomal chromatin was observed, contemporaneously with an increased quantity of Ag-NOR proteins. These ribosomal chromatin changes preceded the beginning of DNA synthesis and were prevented by cycloheximide-induced inhibition of protein synthesis.

Activated ribosomal RNA synthesis in regenerated rat liver upon inhibition of protein synthesis

Cycloheximide (Cyh), administered at a dose of 5 mg/kg body wt blocks protein synthesis in normal rat liver (NRL) and regenerating rat liver (RRL). The rate of synthesis of 45S pre-rRNA in RRL, studied after RNA labelling in vivo is activated 2.8 times. Pre-r RNA synthesis in RRL is more sensitive to the stopped translation, but never falls down to the level in NRL. The major contribution to the rDNA transcription activation in RRL comes from the 20-fold increase in the number of pol I molecules engaged in the transcription, the elongation rate being 1.4-fold accelerated. Cyh quenches partially the enhanced rDNA transcription in RRL: the number of pol I molecules and their elongation rate are about 1.7-fold and 1.5-fold higher, respectively, than the corresponding values in NRL after Cyh treatment. The results show that two different mechanisms control the number and the rate of initiation and elongation of RNA polymerase I in rat liver; one of them depends on continuous protein synthesis and can be inactivated by Cyh, the other is Cyh resistant.

Relationship between interphasic nucleolar organizer regions and growth rate in two neuroblastoma cell lines

The relationship between the quantity of silver-stained interphasic nucleolar organizer regions (NORs) and nuclear synthetic activity, caryotype, and growth rate was studied in two established neuroblastoma cell lines (CHP 212 and HTB 10). Statistical analysis of silver-stained NORs revealed four times as many in CHP 212 cells compared with HTB 10 cells. No difference was observed in the ribosomal RNA synthesis between the two cell lines. The caryotype index was 1.2 for CHP 212 and 1.0 for HTB 10 cells. The number of chromosomes carrying NORs and the quantity of ribosomal genes was found to be the same for the two cell lines. Doubling time of CHP 212 cells was 20 hours compared with 54 hours for HTB 10 cells. In CHP 212 cells bindering of cell duplication by serum deprivation induced a progressive lowering (calculated at 48, 72, and 96 hours) of the quantity of silver-stained interphasic NORs. Recovery of duplication by new serum addition induced, after 24 hours, an increase of the quantity of silver-stained interphasic NORs up to control levels. In the light of available data, these results indicate that the quantity of interphasic NORs is strictly correlated only to the growth rate of the cell.

Endotoxin inhibition of glucocorticoid enzyme induction and in vivo 3H-dexamethasone labelling of rat liver nuclei

1. The effect of endotoxin on glucocorticoid (GC) induction of liver TO and TAT was investigated. 2. It was found that endotoxin inhibited not only TO GC induction, but also that of TAT, though to a lesser extent (17.41%). 3. Endotoxin did not influence the binding capacity of liver cytosol for 3H-dexamethasone at the second hour after the toxin administration. 4. In in vivo experiments endotoxin inhibited with 57.2% the binding of 3H-dexamethasone to hepatic nuclei. 5. It is suggested that the lower extent of endotoxin inhibition of GC induction of TAT may be due to the counteracting action of some inductor(s) for TAT only.

Spatial redistribution of ribosomal chromatin in the fibrillar centres of human circulating lymphocytes after stimulation of transcription

We have studied the distributional changes of the completely extended ribosomal chromatin present in the fibrillar centres of resting human lymphocytes after phytohemagglutinin (PHA) treatment. In thin sections of resting lymphocytes selectively stained for DNA, the extended non-nucleosomal chromatin was located in a solitary, large agglomerate which corresponds to the solitary, large fibrillar centre observed in uranium-lead-stained sections. At 20 h after PHA stimulation the ribosomal chromatin agglomerate appeared to be fragmented into smaller agglomerates which correspond to numerous fibrillar centres surrounded by a thick rim of dense fibrillar component. The mean area of ribosomal chromatin agglomerates from resting lymphocytes was found to be 0.772 mu 2 + 0.125 SD, whereas in stimulated lymphocytes it was found to be 0.184 mu 2 + 0.052 SD. At 20 h after PHA treatment ribosomal RNA (rRNA) synthesis was 8-fold greater than the control value, whereas DNA synthesis had not started. These results indicate that ribosomal chromatin of resting lymphocyte fibrillar centres contains transcribable sequences, temporally not expressed.

Antibodies to histones and disease activity in systemic lupus erythematosus: a comparative study with an enzyme-linked immunosorbent assay and immunoblotting

Enzyme-linked immunosorbent assay (ELISA) and immunoblotting were used to define comparatively the frequency of antibodies to total histones and different histone fractions - H1, H2A, H2B, H3, and H4 - in 16 patients with idiopathic systemic lupus erythematosus. H1 and H2B showed the most prominent antigenic properties; H3's were weaker, while antibodies to H2A and H4 were rarely detected and only with the more sensitive ELISA on microtiter plates. Detailed specification was carried out of the antigenic determinant on fragments obtained by specific cleavage of purified H1 at phenylalanine-106. Antibodies were detected against both the NH2 and COOH terminal halves of the molecule. The presence of antihistone antibodies was not associated with any particular clinical symptoms, but an obvious link with disease activity has been proved.

A dot-immunobinding assay for antimitochondrial antibodies

A dot-immunobinding assay was established for the detection of antimitochondrial antibodies. Nitrocellulose strips were coated with sonicated rat liver mitochondria and incubated in the presence of human sera. The resulting immune complexes were visualized with an enzyme-linked second antibody. Antimitochondrial antibodies were found in the sera of 96% of patients with primary biliary cirrhosis, 17% of patients with autoimmune hepatitis and 4% of patients with progressive systemic sclerosis. Sera of patients with other liver diseases or with systemic lupus erythematosus, specimens positive for M1 and M3 mitochondrial antibodies and samples from normal controls were all negative. Antinuclear and other cytoplasmic antibodies were not detected in this assay. The dot-immunobinding assay for antimitochondrial antibodies is rapid and sensitive, and obviates the need for expensive equipment.

Ribosome biogenesis and nucleolar ultrastructure in neuronal and oligodendroglial rat brain cells

The absolute amounts of precursor to ribosomal RNA (pre-rRNA) and ribosomal RNA (rRNA) in isolated rat brain neuronal and oligodendroglial nuclei were determined. The amount of the major pre-rRNA and rRNA species in neuronal nuclei was about twofold higher than in oligodendroglial nuclei. The relative rate of pre-rRNA synthesis in vivo was 2.3- to 2.7-fold higher in neuronal as compared with oligodendroglial nuclei. This corresponds to a 2.7-fold higher activity of the "template-bound" RNA polymerase I in isolated neuronal nuclei, whereas the activity of the "free" enzyme in both neuronal and glial nuclei was almost identical. The higher transcription rates of rRNA genes correlated with the markedly more prominent fibrillar component in neuronal nucleoli. The turnover times of the major pre-rRNA and rRNA species in neuronal and oligodendroglial nuclei were similar, except for 45S pre-rRNA, which turned over at an approximately 1.5-fold slower rate in neuronal nuclei. The relative rates of processing of pre-rRNA and of nucleocytoplasmic transport of rRNA in neuronal cells were approximately 2.7-fold higher than in oligodendroglial cells and corresponded to the differences in rRNA gene transcription rates. The established ribosome formation features correlated with an abundant (neurons) or exceedingly scarce (oligodendrocytes) nucleolar granular component. The turnover rate of cytoplasmic ribosomes in rat brain neurons was twofold slower than in oligodendrocytes, largely because of the about fivefold higher amount of ribosomes in the cytoplasm of neurons. We conclude that ribosome formation and turnover in neuronal and oligodendroglial cells are adapted to the protein synthetic levels in these two types of brain cells.

Re-utilization of pyrimidine nucleotides during rat liver regeneration

The changes in the specific radioactivities of the pool of total acid-soluble uridine nucleotides and of uridine and cytidine components of total cellular and nuclear RNA were monitored in regenerating rat liver for 12 days after partial hepatectomy. Evidence is presented for the re-utilization of pyrimidine nucleotides derived from cytoplasmic RNA degradation for the synthesis of new RNA. The extent of recycling was assessed and the true rate of rRNA turnover determined more accurately. The reutilization of the uridine components of RNA was 7.0%/day during the proliferative and 3.2%/day during the post-proliferative phase, whereas that of the cytidine nucleotides was more pronounced (9.6%/day and 18.1%/day respectively). The results reveal the existence of partial compartmentalization of pyrimidine ribonucleoside triphosphate pools in the nucleus and cytoplasm of rat liver cells.

Differences in the mode of iodination of H2a variants in chromatin

Modification of H2a variants with radioactive iodine was used to study under different ionic conditions the accessibility of their tyrosine residues in chromatin, in monosomes and when free in solution. The modification of tyrosine 57 in the hydrophobic part of H2a was found responsible for the appearance of new fractions with a reduced electrophoretic mobility in the presence of Trition X 100, detected only by autoradiography (radioactive "ghosts"). At low ionic strength a very small number of molecules were iodinated in chromatin, the modification affecting only their hydrophobic region. At moderate ionic strength the tyrosine residues near the N-terminal region of the molecule were predominantly modified. In chromatin the accessibility of the tyrosine residues of H2a1 was much greater than that of H2a2, a difference not observed with free histones.

Excess 5'-terminal sequences in the rat nucleolar 28S ribosomal RNA

The 5'-termini of purified rat liver nucleolar and cytoplasmic 28S ribosomal RNA (rRNA) are precisely located within the homologous rDNA sequence by S1 nuclease protection mapping using an appropriate rDNA restriction fragment. The 5'-termini of nucleolar 28S rRNA are heterogeneous in length. The bulk of the nucleolar 28S rRNA map within two CTC motifs in rDNA located in the internal transcribed spacer 2 at the 50-60 and 5-15 bp upstream from the site of the homogeneous 5'-terminus of the cytoplasmic 28S rRNA. These results provide direct proof that nucleolar 28S rRNA molecules contain excess sequences at their 5'-termini and require further processing to generate the mature cytoplasmic 28S rRNA.

Mapping of the major early endonuclease cleavage site of the rat precursor to rRNA within the internal transcribed spacer sequence of rDNA

The endonuclease cleavage of 41 S pre-rRNA to yield 32 S and 21 S pre-rRNA constitutes a major early step in the processing of pre-rRNA in rat liver. The 5'-terminus of 32 S pre-rRNA and the 3'-terminus of 21 S pre-rRNA were precisely located within the rDNA sequence by S1 nuclease protection mapping and use of appropriate rDNA restriction fragments. The 5'-terminus of 12 S pre-rRNA, an initial product of 32 S pre-rRNA processing, was also mapped within the rDNA sequence. The 5'-termini of 32 S and 12 S pre-rRNA coincide and map within a 14-residue T-tract (non-coding strand) at 161-163 bp upstream from the 5'-end of the 5.8 S rRNA gene. The 3'-terminus of 21 S pre-rRNA maps within the same T-tract. These results show that the endonuclease cleavage occurs within a U-tract in the internal transcribed spacer 1 sequence of 41 S pre-rRNA. The homogeneity of the 5'- or 3'-termini of 32 S, 12 S and 21 S pre-rRNA indicates also that the terminal processing of these molecules, if any, is markedly slower. The coincidence in the location of 32 S and 12 S pre-rRNA 5'-termini shows further that the endonuclease cleavage of 32 S pre-rRNA precedes the removal of its 5'-terminal segment to yield 5.8 S rRNA. The absence in the whole pre-rRNA internal transcribed spacer of sequences complementary to the target U-tract suggests that the endonuclease cleavage, generating 32 S and 21 S pre-rRNA, occurs in a single-stranded loop of U-residues.

Localization and structure of endonuclease cleavage sites involved in the processing of the rat 32S precursor to ribosomal RNA

The initial endonuclease cleavage site in 32 S pre-rRNA (precursor to rRNA) is located within the rate rDNA sequence by S1-nuclease protection mapping of purified nucleolar 28 S rRNA and 12 S pre-rRNA. The heterogeneous 5'- and 3'-termini of these rRNA abut and map within two CTC motifs in tSi2 (internal transcribed spacer 2) located at 50-65 and 4-20 base-pairs upstream from the homogeneous 5'-end of the 28 S rRNA gene. These results show that multiple endonuclease cleavages occur at CUC sites in tSi2 to generate 28 S rRNA and 12 S pre-rRNA with heterogeneous 5'- and 3'-termini, respectively. These molecules have to be processed further to yield mature 28 S and 5.8 S rRNA. Thermal-denaturation studies revealed that the base-pairing association in the 12 S pre-rRNA:28 S rRNA complex is markedly stronger than that in the 5.8 S:28 S rRNA complex. The sequence of about one-quarter (1322 base-pairs) of the 5'-part of the rat 28 S rDNA was determined. A computer search reveals the possibility that the cleavage sites in the CUC motifs are single-stranded, flanked by strongly base-paired GC tracts, involving tSi2 and 28 S rRNA sequences. The subsequent nuclease cleavages, generating the termini of mature rRNA, seem to be directed by secondary-structure interactions between 5.8 S and 28 S rRNA segments in pre-rRNA. An analysis for base-pairing among evolutionarily conserved sequences in 32 S pre-rRNA suggests that the cleavages yielding mature 5.8 S and 28 S rRNA are directed by base-pairing between (i) the 3'-terminus of 5.8 S rRNA and the 5'-terminus of 28 S rRNA and (ii) the 5'-terminus of 5.8 S rRNA and internal sequences in domain I of 28 S rRNA. A general model for primary- and secondary-structure interactions in pre-rRNA processing is proposed, and its implications for ribosome biogenesis in eukaryotes are briefly discussed.

Different Rates of Synthesis and Turnover of Ribosomal RNA in Rat Brain and Liver

The kinetics of in vivo labeling of cellular free UMP and nucleolar, nucleoplasmic, and cytoplasmic rRNA with [14C]orotate in rat brain and liver were investigated. Evaluation of the experimental data shows: (a) The rate of nucleolar precursors of ribosomal RNA (pre-rRNA) synthesis and the deduced rate of ribosome formation in brain is about fivefold lower than in liver and corresponds to 220-260 ribosomes/min/nucleus. (b) The lower rate of in vivo pre-rRNA synthesis is correlated with a lower activity of RNA polymerase I in isolated brain nuclei. (c) The half-lives of nucleolar rRNA in brain and liver are 210 and 60 min, respectively, thus showing a slower rate of processing of pre-rRNA in brain nucleoli. (d) The nucleo-cytoplasmic transport of ribosomes in brain is also markedly slower than in liver and reflects the lower rates of synthesis and processing of pre-rRNA. (e) Cytoplasmic ribosomes in brain and liver turn over with half-lives of about 6 and 4 days, respectively. It is concluded that the markedly lower rate of ribosome biogenesis in brain is specified mainly at the level of transcription of rRNA genes.

Structural organization of chromatin in nucleolar organizer regions of nucleoli with a nucleolonema-like and compact ribonucleoprotein distribution

We have studied the relationship between the structural organization of intranucleolar chromatin and fibrillar nucleolar structures, fibrillar centers, and RNP fibrillar component, which are the interphase counterpart of metaphase nucleolar organizer regions (NORs), in regenerating rat hepatocytes and in a human tumor cell line (TG cells). These two cell types were characterized by a nucleolonema-like and compact nucleolar RNP distribution, respectively. We found that, in sections selectively stained for DNA, the intranucleolar chromatin composed of extended, nonnucleosomal DNA filaments formed roundish agglomerates with a spatial distribution which was superimposable on that of the fibrillar centers and the RNP fibrillar component around them and on sites of the silver reaction in samples selectively stained for Ag-NOR proteins. The agglomerates of extended nonnucleosomal DNA filaments were small and numerous in regenerating hepatocyte nucleoli, in which the RNP components had a nucleolonema-like distribution, whereas they were large and few in TG cell nucleoli, in which the RNP components showed a compact organization. Since the pattern of ribosomal RNA synthesis and processing was similar in the two cell types, a model was proposed in which the difference in size and shape of the agglomerates of extended DNA might be responsible for the different structural organization of the RNP components.

Post-transcriptional regulation of ribosome formation in the nucleus of regenerating rat liver

Kinetic experiments on RNA labelling in vivo with [14C]orotate were performed with normal and 12h-regenerating rat liver. The specific radioactivities of nucleolar, nucleoplasmic and cytoplasmic rRNA species were analysed by computer according to the models of rRNA processing and nucleo-cytoplasmic migration given previously [Dudov, Dabeva, Hadjiolov & Todorov, Biochem. J. (1978) 171, 375-383]. The rates of formation and the half-lives of the individual pre-rRNA and rRNA species were determined in both normal and regenerating liver. The results show clearly that the formation of ribosomes in regenerating rat liver is post-transcriptionally activated: (a) the half-lives of all the nucleolar pre-rRNA and rRNA species are decreased by 30% on average; (b) the pre-rRNA processing is directed through the shortest maturation pathway: 45 S leads to 32 S + 18 S leads to 28 S; (c) the nucleo-cytoplasmic transfer of ribosomes is accelerated. As a consequence, the time for formation and appearance of ribosomes in the cytoplasm is shortened 1.5-fold for the large and 2-fold for the small subparticle. A new scheme for endonuclease cleavage of 45 S pre-rRNA is proposed, which explains the alterations in pre-rRNA processing in regenerating liver. Its validity for pre-rRNA processing in other eukaryotes is discussed. It is concluded that: (i) the control sites in the intranucleolar formation of 28 S and 18 S rRNA are the immediate precursor of 28 S rRNA, 32 S pre-rRNA, and the primary pre-rRNA, 45 S pre-rRNA, respectively; (ii) the limiting step in the post-transcriptional stages of ribosome biogenesis is the pre-rRNA maturation.

A 12 S precursor to 5.8 S rRNA associated with rat liver nucleolar 28 S rRNA

The pre-rRNA and rRNA components of rat and mouse liver nucleolar RNA were analysed. It was shown that upon denaturation, part of the 32 S pre-rRNA is converted into 28 S rRNA and 12 S RNA. The 12 S RNA from mouse (Mr, 0.36 X 10(6)) is larger than the one from rat (Mr, 0.32 X 10(6). The 12 S RNA chain is intact and resists denaturation treatment. The non-covalent binding of this RNA with nucleolar 28 S rRNA is stronger than that of 5.8 S rRNA with 28 S rRNA. Hybridization with a rat internal-transcribed spacer rDNA fragment identifies 12 S RNA as corresponding to the 5'-end non-conserved segment of 32 S pre-rRNA, including 5.8 S rRNA. The significance of the formation of a 12 S precursor to 5.8 S rRNA in the biogenesis of ribosomes in mammalian cells is discussed.

Relationship between the extended, non-nucleosomal intranucleolar chromatin in situ and ribosomal RNA synthesis

In the present study we have investigated the relationship between the structure of intranucleolar chromatin in situ and the synthesis of rRNA. Using thin sections selectively stained for DNA we observed that intranucleolar chromatin of cortisol-stimulated rat hepatocytes consisted of clumps and fibres, both showing a nucleosomal configuration, and by loose agglomerates of extended DNA filaments, with a thickness of 2-3 nm, which never formed nucleosomal structures. After inhibition of rRNA synthesis by actinomycin D, the agglomerates of extended DNA filaments without nucleosomal configuration were noticed to be still present even at 3 h after drug treatment. In human resting lymphocytes, with a very low rate of rRNA synthesis, a large roundish, loose agglomerate of DNA filaments without nucleosomal configuration was found in the central zone of the nucleolar body. After a 16-fold increase in rRNA synthesis induced by a 48-h stimulation with phytohemagglutinin (PHA) the loose agglomerates appeared to be more numerous, but markedly reduced in size. We concluded that the extended non-nucleosomal configuration is a permanent feature of intranucleolar loose chromatin agglomerates and not a consequence of transcriptional activity.

Turnover of ribosomes in regenerating rat liver

The turnover of ribosomes was studied in regenerating liver and the rates of ribosome degradation in the proliferative (1-5 days) and post-proliferative (6-12 days) phases after partial hepatectomy compared: Ribosome turnover during the first 3 days is slower, the half-life of ribosomes being approximately 300 hr. Ribosome synthesis is markedly activated--39% synthesis rate, which corresponds to 34% accumulation rate per day. The half-life of ribosomes during the second phase is about 107 hr. The rate of synthesis falls down to 19% the net gain of ribosomes being 3% per day.

Acceleration of ribosome formation in rat liver in response to hydrocortisone

The amount of nuclear pre-rRNA (precursor to rRNA) and rRNA species and their labelling in vivo with [14C]orotate were determined in hormone-deficient and treated rats. On the basis of the data obtained, the rates of synthesis and processing of pre-rRNA in the two groups of animals were compared. It is shown that the rate of nucleolar RNA synthesis is increased twice, its half-life is reduced about 1.4 times and the endonuclease processing of primary pre-rRNA is channeled through the shortest maturation pathway. Thus, an accelerated ribosome formation takes place in response to hydrocortisone. The overproduced ribosomes are not retained in the nucleoplasm and are immediately transferred to the cytoplasm.

Transcriptional control of ribosome production in regenerating rat liver

Kinetic experiments of labelling in vivo with [14C]orotate of cellular free UMP and/or UTP, nucleolar, nucleoplasmic and cytoplasmic rRNA in normal and 12 h-regenerating rat liver were performed. The specific-radioactivity curves obtained were analysed by computer and the rates of synthesis of precursor rRNA (45S pre-rRNA) and cytoplasmic 28S and 18S rRNA calculated. (a) The rates of synthesis of 45S pre-rRNA in normal and regenerating rat liver are 1400 and 3700 molecules/min per nucleus respectively; (b) the average rates of formation of mature 28S and 18S rRNA are identical with the rates of synthesis of 45S pre-rRNA in both normal and regenerating rat liver. Thus the synthesis of rRNA in 12h-regenerating rat liver is activated 2.7-fold. The analysis of rRNA synthesis in isolated nucleoli also shows a 2.7-fold stimulation of transcription in regenerating liver. It is concluded that all the 45S pre-rRNA molecules synthesized are processed and transferred as 28S and 18S rRNA in the cytoplasm, i.e. degradation (wastage) of newly synthesized ribosomes in the nucleus does not occur in both normal and regenerating rat liver. Thus the enhanced production of ribosomes in regenerating rat liver is regulated only at the transcriptional level.

Evidence that free polysomes are not the precursors of membrane-bound polysomes in rat liver

We tested, in rat liver, the postulate that free polysomes were precursors of membrane-bound polysomes. Three methods were used to isolate free and membrane-bound ribosomes from either post-nuclear or post-mitochondrial supernatants of rat liver. Isolation and quantitation of 28 S and 18 S rRNA allowed determination of the 40 S and 60 S subunit composition of free and membrane-bound ribosomal populations, while pulse labeling of 28 S and 18 S rRNA with [6-14C) orotic acid and inorganic (32P] phosphate allowed assessment of relative rates of subunit renewal. Throughout the extra-nuclear compartment, 40 S and 60 S subunits were present in essentially equal numbers, but, free ribosomes contained a stoichiometric excess of 40 S subunits, while membrane-bound ribosomes contained a complementary excess of 60 S subunits. Experiments with labeled precursors showed that throughout the extra-nuclear compartment, 40 S and 60 S subunits accumulated isotopes at essentially equal rates, however, free ribosomes accumulated isotopes faster than membrane-bound ribosomes. Among free ribosomes or polysomes, 40 S subunits accumulated isotopes faster than 60 S subunits, but, this relationship was not seen among membrane-bound ribosomes. Here, 40 S subunits accumulated isotope more slowly than 60 S subunits. This distribution of labeled precursors does not support the postulate that free polysomes are precursors of membrane-bound polysomes, but, these data suggest that membrane-bound polysomes could be precursors of free polysomes.

Quantitative alterations in the nucleolar and nucleoplasmic ribosomal ribonucleic acids in regenerating rat liver

A quantitative analysis of the nuclear pre-rRNA (precursor to rRNA) and rRNA in normal and 12h-regenerating rat liver was carried out, and the absolute amounts of the identified pre-rRNA and rRNA species in the nucleolus and nucleoplasm were determined. Characteristic changes in the pre-rRNA and rRNA pool sizes in regenerating liver are found which reveal alternations in both pre-rRNA processing and nucleocytoplasmic transition of ribosomes.

Isolation of active transcription complexes from animal cell nuclei by nitrocellulose binding

A method for the rapid isolation of active transcription complexes from animal cell nuclei is described. The method is based on the observation that, after lysis of nuclei with the detergents Sarkosyl and Triton X-100, transcription complexes are selectively bound to nitrocellulose. The nitrocellulose filters retain 80-90% o the RNA labelled briefly in vitro and about 10% of the nuclear DNA. The bulk of the retained DNA is in the size range of 20 kb. Transcription complexes involving both RNA polymerase I and II are retained by nitrocellulose. The nitrocellulose-bound transcription complexes preserve almost all of their RNA polymerase activity. The size distribution of the RNA product shows that bound transcription complexes retain also most of their growing RNA chains. The possibility to use selective retention by nitrocellulose in the analysis of transcriptionally active genes is discussed.

The nucleotide sequence of the initiation region of the ribosomal transcription unit from mouse

The 5' end of 45S pre-rRNA has been located on a cloned rDNA fragment from mouse by r-loop mapping and the nuclease S1 protection technique. 45S pre-rRNA could be shown to represent the primary transcript of the ribosomal genes because 5' polyphosphate termini have been detected by an enzymatic assay. The sequence of about 1100 nucleotides surrounding the initiation site for ribosomal RNA transcription has been determined. Features of this region of the ribosomal DNA will be discussed. A comparison of the nucleotide sequence with corresponding areas of ribosomal genes from other eukaryotes does not reveal significant homology in the region of transcription initiation.

Ribosomal RNA precursor transcription in rat liver is not dependent on continuous synthesis of proteins

The effect of inhibition of protein synthesis by cycloheximide on rRNA precursor transcription in rat liver was analyzed. Two doses of the drug were studied: low, 5 mg/kg, and high, 20 mg/kg. Both doses of cycloheximide cause rapid, complete and continuous inhibition of protein synthesis. The low dose of the antibiotic does not alter the rRNA precursor transcription for at least 4 h, while the high dose, which is lethal to rats, leads gradually to suppression of rRNA precursor synthesis. It is shown that the high dose of cycloheximide causes profound changes in the metabolism of the free nucleotides and drastic inhibition of [14C]orotate and [32P]orthophosphate uptake into the pool of free nucleotides. It is supposed that the strong side-effects of cycloheximide, rather than the cessation of protein synthesis, are responsible for the observed inhibition of rRNA precursor synthesis. It is concluded that rRNA precursor transcription is not regulated by rapidly turning-over protein(s).

Effect of cycloheximide on the in vivo and in vitro synthesis of ribosomal RNA in rat liver

The action of low (5 mg/kg body wt;) and high (20 mg/kg body wt.) doses of cycloheximide, both causing a rapid and almost complete inhibition of protein synthesis in rat liver is investigated. Short-term (15 min) [14C]orotate incorporation into nucleolar rRNA in vivo is inhibited only by the high dose acting for periods longer than 1 h. The effect may be correlated with a strongly reduced labelling of the cellular pool of free uridine nucleotides. These results indicate that in vivo transcription of rRNA genes may not be under stringent control. The activity of template-bound RNA polymerase A in nuclei isolated from animals treated with both doses of cycloheximide is reduced within 1 h to about 50% of controls reaching nearly plateau levels at longer times of action of the drug. The differential effect of cycloheximide inhibition of protein synthesis on in vivo and in vitro rRNA synthesis suggests the existence of elongation control protein(s) characterized by a rapid turnover and a loose association with the nucleus.

Maturation and nucleo-cytoplasmic transport of rat-liver ribosomal RNA upon D-galactosamine inhibition of transcription

D-Galactosamine (250 mg/kg body weight) causes 90--95% inhibition of [14C]orotate or inorganic [32P]phosphate incorporation in vivo into rat liver nuclear RNA within 30 min. The transcription of both nucleolar and nucleoplasmic genes is inhibited to the same extent. Under these conditions, prelabbeled 45-S pre-rRNA is processed quantitatively to nuclear 28-S and 18-S rRNA. The nucleocytoplasmic transport of both 28-S and 18-S rRNA remains unaltered for about 60 min after blockage of transcription. At this stage the nucleo-cytoplasmic transport of 18-S rRNA is almost completed. It is concluded that formation and nucleo-cytoplasmic transport of ribosomes is independent of concurrent transcription of rRNA or nucleoplasmic genes. At later stages, the nucleocytoplasmic transport of 28-S rRNA is delayed and its partial degaradation in the nucleus may take place. This effect is correlated with a decreased (up to 40% of controls) labelling of nuclear proteins. However, the labelling of total cellular or microsomal proteins remains unchanged up to 3 h after D-galactosamine administration. It is suggested that the last nuclear steps of ribosome formation are dependent on the continuous supply of rapidly-labelled nuclear proteins.

Alterations in the processing of rat-liver ribosomal RNA caused by cycloheximide inhibition of protein synthesis

Cycloheximide given in vivo at low doses (2--5 mg/kg body weight) causes within 30 min a complete inhibition of protein synthesis in rat liver. The labelling of nuclear proteint is also strongly inhibited. Under these conditions, the amount of nucleolar 45-S pre-rRNA and its [14C]-orotate labelling remain unaffected for at least 4 h. These results show that initially the rates of synthesis and processing of 45-S pre-rRNA are not appreciably altered. On the other hand, drastic alterations in the 45-S pre-rRNA processing pathways occur at the early stages of cycloheximide action. Formation of 18-S rRNA is abolished and that of 28S rRNA is reduced to about half the level in control rats. This dichotomy in the production of the two ribosomal particles may be correlated with a block in the formation of 41-S and 21-S pre-rRNA. Generation of 36-S and 32-S pre-rRNA is still taking place, but the rate of their processing to nucleolar 28-S rRNA is decreased, thus causing the accumulation of these two pre-rRNA species. In parallel, processing of 45-S pre-rRNA to an aberrant 39-S rRNA species is markedly enhanced. The results obtained show that the channelling of nucleolar pre-rRNA along alternative processing pathways is under stringent control by the continuous supply of critical protein(s).

Processing and migration of ribosomal ribonculeic acids in the nucleolus and nucleoplasm of rat liver nuclei

Kinetic studies on the labelling in vivo with [14C]orotate of rat liver nucleolar and nucleoplasmic pre-rRNA (precursor of rRNA) and rRNA, isolated from detergent-purified nuclei, were carried out. The mathematical methods used for the computer analysis of specific-radioactivity curves are described. Evaluation of the experimental data permitted the selection of the most probable models for the processing of pre-rRNA and the nucleo-cytoplasmic transfer of rRNA. It was shown that considerable flexibility exists in the sequence of endonuclease attacks at critical sites of 45 and 41 S pre-rRNA chains, resulting in the simultaneous occurrence of several processing pathways. However, the phosphodiester bonds involved in the formation of mature 28 and 18 S rRNA appear to be protected until the generation of their immediate pre-rRNA. The turnover rates and half-lives of all pre-rRNA and rRNA pools were determined. The turnover rate of 45 S pre-rRNA corresponds to the formation of 1100 ribosomes/min per nucleus. The model for the nucleolus-nucleoplasm-cytoplasm migration of rRNA includes a 'nucleoplasm' compartment in which the small ribosomal subparticle is in rapid equilibrium with the respective cytoplasmic pool. At equimolar amounts of nuclear 28 and 18 S rRNA this model explains the faster appearance of labelled small ribosomal subparticles in the cytoplasm simultaneous with a lower labelling of nuclear 18 S rRNA as compared with 28 S rRNA.