Characteristics of nuclear-ribosomal and DNA-like ribonucleic acids differentially extracted by hot-phenol fractionation

IGFBP1 and Follistatin-like 3 genes are significantly up-regulated in expression profiles of the IUGR placenta

To date, the clinicopathological features of intrauterine growth restriction (IUGR) are not clearly understood, and no effective therapy has been established for IUGR. This is the first study that uses microarray analysis to identify differentially expressed genes in the IUGR placenta. The expression profiles of a total of 9121 genes were examined by cDNA microarray analysis, using mRNA from an appropriate gestational age (AGA) placenta and an IUGR placenta from discordant dichorionic twins. Up-regulation of the IGFBP1 and Follistatin-like 3 genes was detected in the IUGR placenta, with a balanced differential degree of 20.7+/-1.3 and 13.1+/-2.1, respectively, while the balanced differential degrees of other genes were 2.6 or less. The expressions of the IGFBP1 and Follistatin-like 3 genes in four single IUGR and four AGA placentas were also examined by RT-PCR. Consistent with our data in discordant chorionic twin placentas, three of four IUGR placentas showed up-regulation of the IGFBP1 and all four IUGR placentas showed upregulation of Follistatin-like 3 genes when compared to the AGA placentas. Our results suggest that IGFBP1 and Follistatin-like 3 are highly up-regulated in IUGR in the placenta. IGFBP1 and Follistatin-like 3 are known critical regulators of fetal growth and differentiation. Pathways associated with these genes might be important for the pathogenesis of IUGR.

Indoleamine 2,3-dioxygenase serves as a marker of poor prognosis in gene expression profiles of serous ovarian cancer cells

PURPOSE

We aimed to find key molecules associated with chemoresistance in ovarian cancer using gene expression profiling as a screening tool.

EXPERIMENTAL DESIGN

Using two newly established paclitaxel-resistant ovarian cancer cell lines from an original paclitaxel-sensitive cell line and four supersensitive and four refractory surgical ovarian cancer specimens from paclitaxel-based chemotherapy, molecules associated with chemoresistance were screened with gene expression profiling arrays containing 39,000 genes. We further analyzed 44 genes that showed significantly different expressions between paclitaxel-sensitive samples and paclitaxel-resistant samples with permutation tests, which were common in cell lines and patients' tumors.

RESULTS

Eight of these genes showed reproducible results with real-time reverse transcription-PCR, of which indoleamine 2,3-dioxygenase gene expression was the most prominent and consistent. Moreover, by immunohistochemical analysis using a total of 24 serous-type ovarian cancer surgical specimens (stage III, n = 21; stage IV, n = 7), excluding samples used for GeneChip analysis, the Kaplan-Meier survival curve showed a clear relationship between indoleamine 2,3-dioxygenase staining patterns and overall survival (log-rank test, P = 0.0001). All patients classified as negative survived without relapse. The 50% survival of patients classified as sporadic, focal, and diffuse was 41, 17, and 11 months, respectively.

CONCLUSION

The indoleamine 2,3-dioxygenase screened with the GeneChip was positively associated with paclitaxel resistance and with impaired survival in patients with serous-type ovarian cancer.

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.

Free pyrimidine nucleotide pool of Ehrlich ascites-tumour cells. Compartmentation with respect to the synthesis of heterogeneous nuclear RNA and precursors to ribosomal RNA

The incorporation of [14C]orotate and [14C]uridine into UMP residues of hnRNA (heterogeneous nuclear RNA) and pre-rRNA (precursors to rRNA) of Eharlich ascites-tumour cells was compared: orotate was incorporated at a markedly higher rate into hnRNA. On the other hand, the rate of incorporation of uridine into pre-rRTNA was even somewhat higher than into hnRNA. The ratio of specific radioactivities of CMP to UMP residues in pre-rRNA and hnRNA was studied. At all times of labelling this ratio was similar for both RNA species independently of the precursor used. On addition of excess unlabelled uridine, the CMP/UMP labelling ratio in both pre-rRNA and hnRNA rose. However, this increase was much more pronounced with hnRNA. It is concluded that nuclear pyrimidine nucleotide pool for RNA synthesis is compartmentalized. The synthesis of hnRNa is supplied preferentially by the large and the small compartment, respectively. A detailed model for the cellular compartmentation of uridine nucleotide precursors to RNA is proposed.U

Chromatin condensation in isolated rat hepatocyte nuclei induced by ribonuclease treatment

Ribonuclease treatment of isolated rat hepatocyte nuclei induced a 75% solubilization in hnRNA, a reduction of the quantity of perichromatin fibrils, and a marked condensation of chromatin.

The metabolism of high-molecular-weight ribonucleic acid in hypothalamic and cortical regions of the developing female rat brain

The regional metabolism of high-molecular-weight RNA in the developing female rat brain was investigated after the intracranial injection of [32P]P1. The synthesis of polyadenylated RNA relative to high-molecular-weight RNA was determined after oligo(dT)-cellulose chromatography of total cellular high-molecular-weight RNA labelled after 4h. In both hypothalamus and cortex this synthesis was significantly higher during the first 10 days post partum than at subsequent ages. In both regions apparently more mRNA is synthesized in the young. The ratio of the specific radioactivity of cytoplasmic high-molecular-weight RNA relative to that of the nucleus, measured after a 48 h period of labelling, was considered to be an index of the nucleocytoplasmic transport of newly synthesized RNA [Berthold & Lim (1976) Biochem. J. 154, 529--539]. In the cortex, nucleo-cytoplasmic RNA transport in rats aged up to 20 days was significantly higher than in older rats, with the maximal value being attained between 16 and 19 days post partum. In contrast, in the hypothalamus, nucleo-cytoplasmic transport of RNA was low during the neonatal period and comparable with that of the mature animal. However, there were two periods of increased transport at later stages of development, the first between 15 and 19 days post partum and the second between 25 and 29 days post partum. These prepubertal changes in the nucleo-cytoplasmic transport of RNA in the female hypothalamus during weeks 3 and 4 post partum are coincident with other reported changes occurring during sexual differentiation. Differences in the timing of the maturational changes of the two brain regions thus appear to be reflected in developmental changes in RNA transport.

Experimental cardiac hypertrophy and the synthesis of poly (A) containing RNA and of myocardial proteins in the rat: the effect of digitoxin treatment

The synthesis of poly(A) containing RNA was increased in heart of non-digitalized and digitalized rats after aortic constriction, the increase being of the same degree as that of the RNA lacking this sequence. No differences were found, either in the absence or presence of polyuridylic acid, in the incorporation of radioactivity into protein by cardiac ribosomes isolated from animals treated differently. It may be concluded, that after the constriction of the aorta the synthesis of mRNA proceeds at a similar rate as that of the bulk RNA, and that the treatment of the animals with digitoxin does not abolish the stimulus for hypertrophy.

Conformational states of 18 S rRNA from HeLa cells detected by gel electrophoresis

Gel electrophoretic analysis has been used to study some of the conformational properties of 18 S rRNA from HeLa cells. After isolation and treatment by heat or denaturants, the mobility of the RNA in 3% acrylamide/0.5% agarose composite gels was found to be altered; often there were two or more distinct components. Several of these forms could be interconverted by heating to 40 degrees C or by use of dimethyl sulfoxide. Although these comformers were easily distinguishable (by their electrophoretic properties), their melting profiles were very similar. Only a single electrophoretic form was detected when electrophoresis was performed at 40 degrees C. The conformational differences observed are probably derived by variations in base pairing and stacking that result when the parent form is cooled.

RNA release from isolated brain cell nuclei: influence of the postnatal cerebral development

A method to measure the "in vitro" RNA release from rat brain cell nuclei was described. Nuclear RNA was prelabelled "in vivo" for 30 or 120 min. In the first case the released RNA was heterogeneous and its electrophoretic mobility was similar to that of cytoplasmic messenger RNAs; nuclei prelabelled for 120 min mostly released the two major species of ribosomal RNAs. The release of mRNAs from the nuclei increased during cerebral development while that of the ribosomal RNAs did not. The increased capacity of the nuclei to release "radidly labelled" RNA with age neither determined an increase of the polysomal population, nor seemed to be dependent on cytoplasmic macromolecules.

Estrogen-induced changes of ribonucleic acid in the rat uterus

The incorporation of [3H]uridine into uterine RNA of immature rats was studied up to 6 h after a single injection of estradiol. Under these experimental conditions, estradiol progressively increased the incorporation of the radioactive precursor into the total RNA. This increase could not be explained by variations in the uptake of [3H]uridine by the tissue. The total RNA and the fractions obtained by differential thermal extraction were analysed by gel electrophoresis. One hour after hormone treatment, a similar increase of incorporation of the labelled precursor in the different RNA species was observed. After a long period of time, [3H]uridine was preferentially incorporated into rRNA as compared to HnRNA and to heterogenous cytoplasmic RNA. Experiments which involved the use of low doses of actinomycin D sufficient to inhibit any rRNA synthesis, confirmed the relatively slight increase in precursor incorporation into non-ribosomal RNA. The distribution of the radioactivity incorporated into the 3 fractions of RNA, obtained by thermal extraction (2 nuclear fractions and 1 cytoplasmic), suggested an increase in the rate of transcription and transport of the RNA during hormonal treatment. The polyA-containing uterine RNA was isolated on a column of oligo(dT)-cellulose and subsequently studied by electrophoresis. There is no preferential incorporation of precursor into the polyA-containing RNA when compared with the total RNA. However, the polyA-containing RNA constitutes the only part of the non-ribosomal RNA whose synthesis continues to increase throughout the period of hormone treatment.

Nucleo-cytoplasmic relationships of high-molecular-weight ribonucleic acid, including polyadenylated species, in the developing rat brain

The metabolism of high-molecular-weight RNA in the nuclear and cytoplasmic fractions of newborn and adult rat brain was investigated after the intracranial administration of [32P]Pi. In young brain, a considerable proportion of the newly synthesized radioactive RNA is transferred to the cytoplasm, in contrast with the adult brain, where there appears to be a high intranuclear turnover. Electrophoretic analysis of the newly synthesized RNA showed that processing of the rRNA precursor to yield the 28S and 18S rRNA may be more rapid in the adult than in the young, although most of the adult rRNA in the nucleus is not transferred to the cytoplasm. In young brain, processing is probably tightly coupled to transport of rRNA into the cytoplasm, so that 28S and 18S rRNA are not subjected to possible degradation within the nucleus. Polyadenylated RNA turns over in concert with high-molecular-weight RNA in the nuclei of the adult rat brain. In the cytoplasm the polyadenylated RNA has a higher turnover rate relative to rRNA. In the young brain the polyadenylated RNA is transferred to the cytoplasm along with rRNA, although polyadenylated RNA is transported into the cytoplasm at a faster rate. The nuclear and cytoplasmic polyadenylated RNA species of young brain are larger than their corresponding adult counterparts. These results suggest that there are considerable changes in the regulation of the nucleo-cytoplasmic relationship of rRNA and polyadenylated RNA during the transition of the brain from a developing replicative phase to an adult differentiated and non-dividing state.

Three distinct forms of nuclear poly(A) polymerase

Poly(A) polymerase activities have been solubilized from rat liver nuclei and purified by chromatography on Bio-Gel A-1.5M, DEAE-Sephadex and CM-cellulose. Three distinct forms of nuclear poly(A) polymerase have been resolved by chromatography on CM-cellulose. According to their sequence of elution from CM-cellulose these enzyme activities have been termed A, B and C. Enzymes A and B are Mn2+ -dependent, enzyme C requires Mg2+. With the same chromatographic step on CM-cellulose the Mn+ -dependent poly(A) polymerase activities were separated from a Mn2+ -dependent enzyme system capable of synthesizing RNA-primed poly(U), poly(G) and poly(C). The effect of different nuclear and cytoplasmic RNA primers on the rate of poly(A) formation suggests enzyme A to be responsible for the elongation of preexisting poly (A) chains. The phosphorylated derivated derivative of cordycepin, 3'-deoxyadenosine 5'-triphosphosphate (3'-dATP), which is known to inhibit nuclear poly(A) synthesis in vivo, also impairs poly(A) formation in vitro. It is shown that 3'-dATP very probably is not incorporated into poly(A)invitro, suggesting that 3'-dATP primarily affects the catalytic activities of the poly(A) polymerase species rather than directly blocking chain elongation.

Precursor mRNA from erythroid-enriched bone-marrow cells of the rabbit. Electron microscope investigation of precursor mRNA molecules, molecular weight about 1.7 X 10(7), containing mRNA-like structures at one end

Precursor mRNA (pre-mRNA) molecules, sedimenting at greater than 45 S, from erythroid-enriched bone marrow cells of the rabbit and hemoglobin mRNA molecules from rabbit reticulocytes were investigated by electron microscopy. Four of 98 measured pre-mRNA molecules had a length between 15 and 17.1 mum. In some of the pre-mRNA molecules a characteristic condensed structure was observed at one end, strikingly resembling the structure of the mRNA molecules.

The phosphorylation of nuclear proteins in the regenerating and premalignant rat liver and its significance for cell proliferation

In liver regeneration or neoplastic transformation, phosphorylation of nuclear proteins is stimulated. In the regenerating liver all main histone fractions are involved in this process. The type of histone phosphorylated seems to be dependent on the position of the partially synchronized cells within the generation cycle. At a time when most cells are exhibiting maximum HnRNA-synthesis, histone F2a2 belongs to those fractions with highly stimulated phosphate incorporation. Phosphorylation of this fraction alone is stimulated by cyclic AMP in parallel to a stimulation of HnRNA-synthesis. The preneoplastic liver is characterized by oscillating phosphorylation and dephosphorylation reactions of nearly all histone fractions during the first days of N-nitroso-diethylamine administration. After 2 months of carcinogen feeding a 50-150% stimulation of the phosphorylation of Fl subfractions is observed. The phosphate content of the other histones, however, has returned to the original level. A series of further proteins, isolated together with the histones, show very similar phosphorylation characteristics. These proteins are mostly of non-histone origin. It is suggested that some of them are responsible for the transport of RNA with messenger properties within the cell.

Effect of the exotoxin of Bacillus thuringiensis on the biosynthesis and maturation of mouse liver nuclear RNA

The effect of the exotoxin of Bacillus thuringiensis on the in vivo incorporation of [14-C] orotic acid into mouse liver nuclear rRNA and low molecular weight RNA was studied. The following results were obtained. 1. The exotoxin does not inhibit the synthesis of 45 S pre-rRNA, but causes a breakdown of these molecules. 2. The exotoxin inhibits the conversion of 38 S pre-rRNA into 32 S and 21 S. 3. The exotoxin inhibits the labelling of nuclear 5 S RNA, whereas the labelling of 4.6 S pre-tRNA is not affected. It is suggested that 5 S RNA may control the processing of 45 S pre-rRNA.

RNA - DNA hybridization on membrane filters with fragmented mammalian DNA

The possibilities of using fragmented mammalian DNA for hybridization on membrane filters were investigated. The adsorption and release of fragmented DNA were studied as influenced by various factors of the hybridization procedure. It was found that working with preparations sufficiently homogeneous in molecular weight with fragment size 4.8-6.5 S, dissolved in 6 times SSC at neutral pH, the adsorption on filters was almost 100%. After incubation of filters for 18 h in 2 times SSC at 65 degrees C about 50% of the fragmented DNA and 20% of the high molecular weight DNA were released. The degree of release differed for the different families of repeated DNA sequences. Lowest release was obtained with the highly repeated DNA (20%) and highest with the unique DNA (63%), i.e. the release was inversely proportional to the renaturation rate of DNA. In the course of release of fragmented total DNA the material remaining on the filters became enriched in highly repeated sequences, due to selective release of the slowly reassociating fractions. As a result, the percentage of fragmented DNA which hybridized with heterogeneous nuclear RNA was higher than that of high molecular weight DNA. The thermal stabilities of the hybrids with fragmented and high molecular weight DNA were identical. The conditions are defined which permit application of the membrane filter hybridization technique to fragmented mammalian DNA.

Effects of gamma-irradiation on biosynthesis of different types of ribonucleic acids in normal and regenerating rat liver

1. The effect of gamma-irradiation (4000rd) on the synthesis of ribosomal (pre-rRNA) and heterogeneous nuclear RNA (pre-mRNA) in normal and in regenerating rat liver was studied by using 40 min labelling with [6(-14)C]orotic acid. 2. Partial hepatectomy caused a sharp transient increase in the specific radioactivity of the endogenous low-molecular-weight RNA precursors in the livers of both normal and irradiated rats. Irradiation of intact animals did not affect the pool. 3. Irradiation enhanced the synthesis of pre-rRNA for at least 12h. The synthesis of pre-mRNA was also enhanced, but only in the first 3h after irradiation. 4. Partial hepatectomy strongly stimulated the synthesis of both pre-rRNA and pre-mRNA. 5. The synthesis of pre-rRNA was enhanced also in regenerating liver of animals irradiated before or after the operation. The conclusion can be drawn that the early increase in the synthesis of ribosomal RNA is a non-specific cellular response to different injuring factors. 6. The only case where irradiation caused an early inhibition of RNA synthesis was that of pre-mRNA in regenerating liver. This supports the hypothesis that ionizing radiation does not suppress the transcription per se but affects the mechanisms of activation of new genes (cellular programming).

The action of alpha-amanitin in vivo on the synthesis and maturation of mouse liver ribonucleic acids

alpha-Amanitin acts in vitro and in vivo as a selective inhibitor of nucleoplasmic RNA polymerases. Treatment of mice with low doses of alpha-amanitin causes the following changes in the synthesis, maturation and nucleocytoplasmic transfer of liver RNA species. 1. The synthesis of the nuclear precursor of mRNA is strongly inhibited and all electrophoretic components are randomly affected. The labelling of cytoplasmic mRNA is blocked. These effects may be correlated with the rapid and lasting inhibition of nucleoplasmic RNA polymerase. 2. The synthesis and maturation of the nuclear precursor of rRNA is inhibited within 30min. (a) The initial effect is a strong (about 80%) inhibition of the early steps of 45S precursor rRNA maturation. (b) The synthesis of 45S precursor rRNA is also inhibited and the effect increases from about 30% at 30min to more than 70% at 150min. (c) The labelling of nuclear and cytoplasmic 28S and 18S rRNA is almost completely blocked. The labelling of nuclear 5S rRNA is inhibited by about 50%, but that of cytoplasmic 5S rRNA is blocked. (d) The action of alpha-amanitin on the synthesis of precursor rRNA cannot be correlated with the slight gradual decrease of nucleolar RNA polymerase activity (only 10-20% inhibition at 150min). (e) The inhibition of precursor rRNA maturation and synthesis precedes the ultrastructural lesions of the nucleolus detected by standard electron microscopy. 3. The synthesis of nuclear 4.6S precursor of tRNA is not affected by alpha-amanitin. However, the labelling of nuclear and cytoplasmic tRNA is decreased by about 50%, which indicates an inhibition of precursor tRNA maturation. The results of this study suggest that the synthesis and maturation of the precursor of rRNA and the maturation of the precursor of tRNA are under the control of nucleoplasmic gene products. The regulator molecules may be either RNA or proteins with exceedingly fast turnover.