Quantification of hepatic transcribing RNA polymerase molecules, polyribonucleotide elongation rates and messenger RNA complexity in fed and fasted rats

Precipitation of kidney myosin IIA and IIB by freezing

Actomyosin precipitation is a critical step in the purification of myosins. In this work, the objective was to precipitate rat kidney actomyosin and isolate myosin by freezing and thawing the soluble fraction. Kidney was homogenized in imidazole buffer, centrifuged at 45000 g for 30 min, and the supernatant was frozen at -20°C for 48 h. The supernatant was thawed at 4°C, centrifuged at 45000 g for 30 min and the precipitate washed twice with imidazole buffer pH 7.0 (with and without Triton X-100, respectively). The resulting precipitate presented a polypeptide profile in SDS/PAGE characteristic of actomyosin and expressed Mg- and K/EDTA-ATPase activity. The actomyosin complex was solubilized with ATP and Mg, and the main polypeptide, p200, was purified in a DEAE-Sepharose column. p200 was marked with anti-myosin II, co-sedimented with F-actin in the absence, but not in the presence, of ATP and was identified by MS/MS with a high Mascot score for myosin IIA. The analysis identified peptides exclusive of myosin IIB, but detected no peptides exclusive of myosin IIC.

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel statistical approaches, we evaluated the coverage of annotated features of the genome and of candidate processed transcripts, including splice junctions, trans-spliced leader sequences, and polyadenylation tracts. The data provide experimental support for >85% of the annotated protein-coding transcripts in WormBase (WS170) and confirm additional details of processing. For example, the total number of confirmed splice junctions was raised from 70,911 to over 98,000. The data also suggest thousands of modifications to WormBase annotations and identify new spliced junctions and genes not part of any WormBase annotation, including at least 80 putative genes not found in any of three predicted gene sets. The quantitative nature of the data also suggests that mRNA levels may be measured by this approach with unparalleled precision. Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei.

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.

Response of skeletal muscle RNA polymerases I and II to tumour growth

The muscle wasting which occurs in animals bearing a transplantable tumour is accompanied by a decrease in the level of protein synthesis and a loss in RNA. This paper examines the behaviour of RNA polymerases I and II (EC 2.7.7.6) in nuclei isolated from skeletal muscle of rats bearing a Walker 256 carcinoma. Marked decreases were observed in template-engaged RNA polymerase I and II activities and in free RNA polymerase I activity. Free RNA polymerase II activity was unaltered. When assays were carried out at high (NH4)2SO4 concentration or in the presence of heparin the diminished RNA polymerase I activity was still apparent, but heparin and high ionic strength overcame the inhibition of RNA polymerase II. Loss of RNA polymerase I activity was associated with a decrease in the number of template-engaged enzyme molecules and in the polynucleotide elongation rate. The number of template-engaged RNA polymerase II molecules was unaltered by tumour growth, but the polynucleotide elongation rate was significantly reduced. No evidence was obtained for any alteration in ribonuclease activity in nuclei or whole muscles of tumour-bearing rats. These results demonstrate an effect of the tumor on transcription in skeletal muscle of its host.

Transcription of liver ribosomal RNA: differential effect of 5-fluorouracil depending on the nutritional state of mice

The effect of 5-fluorouracil (5-FUra) on RNA transcription in mice liver cells was studied using animals exposed to different nutritional conditions as a model of normal, nondividing cells. There are two levels of rRNA transcription in mouse liver: a basal level found in mice fed on a complete diet (control mice) and a higher level, two- to three-fold increased over the basal, found in mice fed on a protein-depleting diet for about 3 days and refed on a complete diet for at least 5 hr (refed mice). The rRNA transcription was measured as the activity of RNA polymerase I in isolated liver nuclei. It was found that the intraperitoneal administration of 5-FUra (30 mg/kg body wt) to refed mice rapidly decreases the higher level of rRNA transcription towards the basal level. This is accomplished through a decrease of the initiation frequency of rRNA chains by RNA polymerase I. 5-FUra however, does not affect the basal level of rRNA transcription in liver from mice fed on a complete diet. Under this condition the drug does not affect the initiation frequency of rRNA chains. The effect of 5-FUra on rRNA transcription in refed mice is not mediated by an inhibition of protein synthesis.

Effect of cytokinins on ribosomal RNA gene expression in excised cotyledons of Cucurbita pepo L

Excised pumpkin (Cucurbita pepo L.) cotyledons were used to investigate the effects of two different types of cytokinins: N(6)-benzyladenine and N1-(2-chloro-4-pyridyl)-N2-phenylurea on RNA synthesis in isolated nuclei. Treatment of cotyledons with both cytokinins resulted in a rapid enhancement of nuclear RNA-polymerase-I activity (EC 2.7.7.6). Maximum stimulation of RNA polymerase I, responsible for rRNA synthesis, was observed 4-6 h after the start of cytokinin action. The activity of RNA polymerase II was stimulated much more slowly and to a lesser extent. Uridine 5'-monophosphate-uridine analysis of the alkalidigested nascent pre-rRNA chains showed that the stimulation of RNA-polymerase-I activity was the consequence of an increase of the polyribonucleotide-clongation rate. No significant change in the number of transcribing enzyme molecules was defected after hormone treatment (86·10(3) RNA-polymerase-I molecules per diploid genome).Indications that de-novo protein synthesis is necessary for cytokinin-mediated RNA-polymerase stimulation were derived from experiments showing inhibition by cycloheximide.

Eukaryotic ternary transcription complexes: transcription complexes of RNA polymerase II are associated with histone-containing, nucleosome-like particles in vivo

Using a psoralen crosslinking, radioactive labelling technique, we have previously been able to study ternary transcription complexes containing DNA-dependent RNA polymerases I and II which are released from rat liver nuclei by endogenous nuclease digestion [Sargan and Butterworth, refs 1 and 2]. Although the DNA component of these complexes was found to have a 'nucleosome-like' size profile and although the experimental conditions for autodigestion were designed to minimise histone rearrangement, it is necessary to provide further evidence that the periodicity of nuclease cutting around these transcription complexes is conferred by histones. Studies using secondary nuclease digestion of the released transcription complexes now show a digestion barrier characteristic of that conferred by nucleosomal histones which is lost if histones are removed from the complexes. Furthermore, antibodies raised against histones are effective in precipitating transcription complexes of RNA polymerase II and, to a lesser extent, of RNA polymerase I. The data suggest that, in rat hepatic tissue, transcription complexes are in very close proximity (within a few hundred base pairs) of histone-containing, nucleosome-like particles in vivo.

Glucocorticoids modify the rate of ribosomal RNA synthesis in rat thymus cells by regulating the polymerase elongation rate

The mechanism by which glucocorticoids inhibit RNA polymerase A activity, and hence rRNA synthesis, in rat thymus cells has been investigated. Studies of the intranuclear distribution of RNA polymerase A between chromatin bound ("engaged") and unbound ("free") forms revealed that the steroid-mediated inhibition of the activity of the "engaged" form of the enzyme was not accompanied by significant changes in "free" pool activity. In the presence of rifamycin AF/0-13, an inhibitor of re-initiation of RNA polymerase A, the rate of [3H]UMP incorporation into RNA was slower in nuclei from steroid-treated cells than in those from control cells, although in both conditions similar plateau levels of UMP incorporation were attained. Direct measurements of the numbers of transcribing RNA polymerase A molecules and of elongation rates showed that the inhibition of pre-rRNA synthesis was the result of a decrease in enzyme elongation rate; no significant change was observed in the number of transcribing enzymes. The steroid-induced inhibition of pre-rRNA synthesis was selectively abolished by mild proteolysis of nuclei, suggesting the involvement of a labile, regulatory glucocorticoid-induced protein. It is concluded that glucocorticoid treatment of rat thymus cells decreases 45S rRNA synthesis primarily by decreasing the polyribonucleotide elongation rate of RNA polymerase A, possibly by modification of the enzyme.

Differential changes of tightly chromatin-bound RNA polymerase II in starved and cycloheximide-treated rat liver nuclei

In order to investigate the physiological function of loosely and tightly chromatin-bound RNA polymerase II in vivo (1), the changes of these enzyme activities in cycloheximide-treated or starved rat liver nuclei were studied. Total nuclear mRNA synthesis activity in starved rats was considerably decreased, but that of cycloheximide-treated rats was not affected significantly. In starved rats, tightly bound enzyme activity was much more repressed as compared with that of loosely bound enzyme. On the other hand, cycloheximide-treated rats showed the reverse relationship. Thus, mRNA synthesis activity in hepatic nuclei seems to be dependent on the tightly bound RNA polymerase II activity. However, the difference of nuclear mRNA synthesis in both cases can not be explained by the change of chromatin-bound enzyme activity of Yu (2).

Mechanism of enhanced RNA synthesis in acute-phase rat liver and its relationship to chromatin structure

Nuclei isolated from the liver of rats undergoing an acute inflammatory reaction induced by turpentine treatment show increased RNA synthesis. This increase is essentially determined by a faster polyribonucleotide-elongation rate while the number of transcribing polymerase molecules is unchanged. The sensitivity of chromatin to micrococcal-nuclease digestion and the composition of chromosomal proteins are not affected by the acute-phase process. Therefore the increased RNA synthesis by liver nuclei from acutely inflamed rats does not seem to correlate with major changes in chromatin structure.

Non-random effect on RNA synthesis in liver chromatin by administration of dimethylnitrosamine to mice

The effect of dimethylnitrosamine on functional activities of liver chromatin was studied in mice. After a single dose of dimethylnitrosamine injected i.v. (25 mg/kg body wt, 45 min before sacrifice) liver nuclei were isolated and incubated with micrococcal nuclease (EC 3.1.4.7) to an acid-solubility of 2.5% of total DNA. Chromatin was fractionated into a 1,200 g pellet P1, 102,000 g pellet P2 and supernatant fraction S2. Chromatin-bound RNA polymerase I plus III activity decreased 15% in the P1 and 25% in the P2 fraction. No changes in activity were observed in the S2 fraction. Chromatin-bound RNA polymerase II activity decreased 19% in the P1, 49% in the P2 and 32% in the S2 fraction. Heparin stimulated RNA polymerase II activity decreased 10% in the P1 and 44% in the P2 fraction. Formation of initiation in nuclear lysates with RNA polymerase from Escherichia coli increased after administration of dimethylnitrosamine suggesting an increase in the number of sites available for the start of new RNA chains. The results show that limited digestion of nuclei with endonuclease cleaves chromatin regions which are more affected by dimethylnitrosamine than the total chromatin suggesting a non-random effect of the hepatotoxin on chromatin. Modifications of the DNA template by dimethylnitrosamine is indicated by the change in number of initiation complexes.

Starvation and hypothyroidism exert an overlapping influence on rat hepatic messenger RNA activity profiles

To assess the effect of starvation and to explore the potential interrelationship of starvation and thyroid status at the pretranslational level, we have analyzed by two-dimensional gel electrophoresis, the hepatic translational products of starved and fed euthyroid and hypothyroid rats. 5 d of starvation resulted in a statistically significant change in 27 of 240 products visualized, whereas hypothyroidism caused a change in 20, both in comparison with the fed euthyroid state. Of considerable interest was that 68% of all changing messenger (m)RNA sequences were common to the hypothyroid and starved groups and showed the same directional shift. Further, both starvation and hypothyroidism yielded comparable decreases in total hepatic cytoplasmic RNA content. Although it has been well established that the level of circulating triiodothyronine (T3) and the level of hepatic nuclear receptors fall in starvation, this reduction cannot account for the observed decrease of total hepatic RNA nor for all of the alterations in the concentrations of specific mRNA sequences. Thus, administration of T3 to starved animals in a dose designed to occupy all nuclear T3 receptors fails to prevent the fall in total RNA and the majority of starvation-induced changes in the level of mRNA sequences. Moreover, starvation of athyreotic animals results in a further decrease in total RNA and in a further change in the level of individual mRNA species. We conclude, therefore, that although the reduced levels of circulating T3 and the nuclear T3 receptors can contribute to the observed results of starvation, the starvation-induced changes are not exclusively mediated by this factor. The striking overlap in the genomic response between hypothyroid and starved animals raises the possibility that those biochemical mechanisms regulated at a pretranslational level by T3 are either not helpful or injurious to the starving animal. The reduction in circulating T3 and nuclear receptor sites together with T3-independent mechanisms initiated in the starved animal may constitute redundant processes designed to conserve energy and substrate in the nutritionally deprived organism.

A study of lactate dehydrogenase levels and turnover rates during postnatal development in the rat

Specific radioimmunoassays for lactate dehydrogenase A and B subunits have been employed to quantify cellular contents of these proteins more precisely than hitherto possible and to monitor changes during postnatal development. Liver, skeletal muscle, heart muscle and kidney cortex all demonstrated alterations in cellular levels of lactate dehydrogenase subunits over the first 56 days of life, the particular pattern being specific to each tissue. Studies on the turnover of lactate dehydrogenase in vivo and in vitro indicated that the developmental changes in total lactate dehydrogenase content in liver and kidney were regulated at some point(s) during both the biosynthesis and the degradation of the proteins.

Cell repair after liver injury: an analysis of some metabolic conditions required for the stimulation of RNA synthesis in postischemic liver nuclei

Nuclei isolated from liver cells recovering from reversible (non-necrogenic) ischemia show an increased RNA synthesis. The postischemic effect is not abolished by previous adrenalectomy and occurs in fasted as well as in fed animals. Treatment with cycloheximide, at a dose that severely inhibits protein synthesis without primary effects on RNA synthesis, suppresses the postischemic stimulation of RNA synthesis even if cycloheximide is administered when stimulation is already well developed. Postischemic liver nuclei respond only weakly to the additional stimulation of RNA synthesis caused by the presence of cytosol and albumin in the incubation medium.

Control of activation of liver RNA polymerase I occurring after re-feeding of protein-depleted mice

Shortly after feeding protein-depleted mice with a meal containing protein, the RNA polymerase I activity in isolated liver nuclei shows a 2-fold increase over the values in the nuclei of either normal or protein-depleted mice. The activity of the RNA polymerase I solubilized from nuclei of re-fed mice was slightly enhanced, probably reflecting an increase in enzyme amount. However, this increase only accounts for about 30% of the stimulation of transcription in the intact nuclei. Administration of pactamycin, an inhibitor of protein synthesis, to normal or protein-depleted mice has almost no inhibitory effect on the RNA polymerase I activity in the isolated nuclei. On the contrary, within 15 min after treatment with the drug, the stimulated activity in nuclei from re-fed mice declines towards the values in normal or protein-depleted mice and then remains constant. The activity of the solubilized enzyme remains slightly elevated for at least 2 1/2 h after re-fed mice are treated with pactamycin. These observations indicate that the stimulation of the RNA polymerase I activity in the intact nuclei after re-feeding is controlled by mechanisms other than an increase in the enzyme amount and suggest the presence of short-lived proteins required for inducing an activated state of transcription.

Experimental studies on the quality of food proteins

1. This paper reviews chemical and biological assays for measuring the quality of food proteins. 2. The availability of amino acids in a protein is determined by digestability and the capacity of the recipient animal to absorb the amino acids. 3. Intracellularly amino acid concentration influences enzyme activities associated with amino acid and nitrogen metabolism. 4. Amino acids utilized for metabolism affect the cells at the gene level: transcription of DNA to RNA and translation of RNA to protein. 5. More accurate measurements of amino acid utilization for metabolism will follow from further understanding of basic cellular metabolic events.

RNA synthesis and number of transcribing polymerase molecules in ischemic liver nuclei

Nuclei isolated from ischemic liver show a consistent reduction of their RNA synthesis. The reduction persists at high ionic strength and in the presence of heparin, when RNA synthesis in vitro is fully activated and occurs in the presence as well as in the absence of alpha-amanitin. Both the number of transcribing polymerase molecules and the rate of elongation of initiated polynucleotide chains seem to be equally affected.

Current concepts: III. Molecular aspects of dietary modulation of transcription and enhanced longevity

Dietary restriction is a known means of prolonging the life span of animals. How diet can increase longevity at the molecular level is not yet known. As organisms age, there is a decrease in the ability ot synthesize RNA and a decrease in protein synthesis indicating that there is an overall loss in gene expression. In addition, a decrease in protein turnover is evident indicating a lack of cellular renewal because of the accumulation of tissue protein. Evidence is presented in this review, that certain dietary regimens appear to be capable of enhancing the synthesis of mRNA and probably also produce enhanced turnover of tissue proteins. It is proposed that the physiological "stress" produced by restricted feeding paradigms can enhance gene expression and that this may be a significant factor in the maintenance of cellular homeostasis for a longer period of time.

A simple solubilization method for loosely and tightly chromatin-bound RNA polymerase II from rat liver nuclei

Rat liver chromatin-bound RNA polymerase II could be differentially solubilized into two distinct populations, loosely and tightly bound enzymes, by a simple method. By this method the recovery of the solubilized enzyme from the chromatin fraction could be increased considerably as compared with the procedure of Yu (1). The two chromatin-bound enzymes had different properties: (a) Loosely bound enzyme was easily extractable from chromatin with relatively mild ionic condition (0.5 M NaCl); the tightly bound enzyme had to be solubilized by more drastic conditions such as sonication or nuclease treatment. (b) Loosely bound enzyme could not efficiently transcribe the chromatin template, but the tightly bound enzyme was active toward the same template. The latter enzyme is involved in the tight complex with the RNA synthesis activating factors. (c) Cycloheximide treatment in vivo suggests that the two enzymes have different turn-over rates. Therefore, with this simple solubilization method the functionally different two chromatin-bound RNA polymerase II activities can be estimated.

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.

Partial characterization of RNA polymerase II complex released by micrococcal nuclease digestion of rat liver nuclei

Two forms of RNA polymerase II were released from rat liver chromatin by micrococcal nuclease digestion of the nuclei. One from behaved like a free RNA polymerase II and the other like a complex with other nuclear components. Both forms of RNA polymerase II activity were recovered in the 0.16 M NaCl-soluble fraction of the nuclear digest, and the complexed from the RNA polymerase II could transcribe its endogenous template under conditions permitting only of elongation of the RNA synthesis. The RNA polymerase II complex was further purified by gel filtration chromatography and column electrophoresis. Analysis of protein and DNA of the partially purified complex suggested that the RNA polymerase II was bound to mono- or dinucleosomes carrying some characteristic nonhistone proteins. Furthermore, in experiments on tissues from starved rats, the two forms of RNA polymerase II were found to originate from different functional states of the chromatin-bound enzyme in vivo.

Increased transcription and decreased degradation control and recovery of liver ribosomes after a period of protein starvation

In the livers of 5-days-protein-depleted mice there is a decrease of 47% of the ribosome mass. When these animals are fed with an adequate diet, ribosome content is restored to the normal value after 1 day of re-feeding. The mechanisms underlying this phenomenon were studied. It was found that: (1) the activity of RNA polymerase I in the nuclei of livers from re-fed animals showed an enhancement of about 2-fold compared with the activity in normal and protein-depleted liver nuclei; (2) ribosome degradation, measured by the disappearance of radioactivity from ribosomal proteins previously labelled by the administration of NaH14CO3 to the mice, stopped during the first day after re-feeding.

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.

The use of rat liver nucleoplasm for the characterization of heterogeneous nuclear ribonucleic acid synthesis in vitro

1. A nucleoplasmic fraction rich in endogenous RNA polymerase II activity was isolated from rat liver nuclei and conditions were determined under which elongation of RNA molecules initiated in vivo continued at maximal rates in vitro. 2. Elongation rates in vitro were calculated to be about 0.25 nucleotide/s and there were about 7 X 10(3) RNA molecules in the process of being elongated by form-II RNA polymerase per original nucleus. 3. Evidence was obtained suggesting that transcription-dependent release of RNA polymerase II molecules from the template occurred during the incubations in vitro. 4. The nascent RNA was tightly associated with protein and banded as ribonucleoprotein in caesium salt gradients. 5. RNA molecules labelled in vitro were up to 13000 nucleotides in length, but consisted of long unlabelled chains transcribed in vivo with only short labelled sequences added in vitro, and without significant polyadenylation. 6. Hybridization of transcripts in the presence of a vast excess of DNA demonstrated that both form-II RNA polymerase and another enzyme, resistant to low alpha-amanitin concentrations, were synthesizing RNA molecules complementary to both reiterated and unique DNA sequences in the genome.