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PubMed1981

Liver and kidney nuclear RNA synthesis and modifications in dimethylnitrosamine-treated rats.

RNA synthesis was measured in nuclei isolated from rat liver and kidney 22 h post injection of 30 mg dimethylnitrosamine/kg body weight. In nuclear preparations were shown by electron microscopy to consist of clean hepatocytes and the liver nuclei showed no apparent necrosis at that time. In vitro RNA synthesis and methylation were proportional to time and nuclear concentration, as well as dependent on exogenous nucleoside triphosphates and S-adenosylmethionine. 60-70% of the in vitro synthesis was inhibited by 1 microgram/ml alpha-amanitin. Total liver nuclear RNA synthesis was increased after dimethylnitrosamine exposure, but, unlike RNA synthesis in nuclei after partial hepatectomy, both alpha-amanitin-sensitive and -resistant synthesis were increased. Differences were found between dimethylnitrosamine-treated liver and kidney nuclear RNA synthesis which was sensitive to inhibition by 1-10 microgram/ml alpha-amanitin, presumably a product of RNA polymerase III. Nuclear RNA methylation with S-adenosylmethionine, which was dependent on new RNA synthesis, differed between dimethylnitrosamine-treated rat liver and kidney nuclei. The endogenous RNA methyl substituents labeled in vitro showed differences in levels of methylation of bases, the 2'-O position of ribose and caps in comparison between control and dimethylnitrosamine-treated nuclei from both liver and kidney. Significant differences were obtained in both nuclear RNA transcription and methylation in vitro between the two tissues in response to pretreatment of the rat in vito dimethylnitrosamine.

Animals↗
PubMed1995

RNA-protein interactions in the ribonucleoprotein T-complexes in a mitochondrial extract from Leishmania tarentolae.

We have investigated protein-RNA interactions and the incorporation of [alpha-32P]UTP into the guide RNA and mRNA components of the 'T-complexes' in a mitochondrial extract from Leishmania tarentolae. The terminal uridylyl transferase-containing complex T-IV is probably involved in the maturation of the 3'-oligo(U) tail of the gRNAs, but the biological function and biochemical nature of the remaining T-complexes is not known. We have found that the relative extent of labeling of the RNA components is dependent on the UTP concentration: at low levels, the main endogenous RNA components labeled are the gRNAs in T-IV; at higher levels, the mRNAs in all of the T-complexes are preferentially labeled. We also show a tentative correlation in the migration pattern of UTP-labeled T-complexes and complexes which bind exogenous labeled RNA. The relative extent of binding to specific complexes is dependent upon the type of RNA. Most of the interactions between the labeled RNAs and proteins can be disrupted by heparin or a large excess of rRNA, but two labeled complexes were resistant to competition. Most of the binding of labeled exogenous gRNA is disrupted by competition with a large excess of rRNA, but predigestion of the extract with micrococcal nuclease and saturation with rRNA uncovered a high affinity complex, which involves at least two proteins interacting with the bound gRNAs. A knowledge of the RNA and protein components may aid in understanding the biological roles of these RNP complexes.

Animals↗
PubMed1977

Distribution and expression in mammals of genes ralated to an endogenous type C RNA virus of Odocoileus hemionus.

An endogenous type C virus recently isolated from the Columbian black-tailed deer (Odocoileus hemionus) was used as a molecular probe to study the distribution of virus-related nucleotide sequences in cellular DNAs of mammalian species. By DNA-DNA hybridization, the most extensive homology was demonstrated between the viral complementary DNA and cellular DNA isolated from Odocoileus species. DNAs of representatives of other genera within the same family, Cervidae, were partially related to the virus, consistent with the phylogenetic relationship of these species to Odocoileus. O. hemionus viral sequences were also detected within cellular DNAs of members of a more distantly related artiodactyl family, Bovidae. These findings suggest the genetic transmission of type C viral genes within cervids and bovids for a period of at least 25 to 30 million years. There was no detectable nucleotide sequence homology between O. hemionus virus and representatives of other major groups of mammalian type C viruses. These results indicate that despite the known antigenic relatedness of mammalian type C viruses, the O. hemionus virus has diverged sufficiently to be considered the prototype of a separate group. By radioimmunological techniques, it was possible to detect and partially purify, from normal tissues of cervid species, antigens related to the major structural protein of the O. hemionus virus. The present findings, that O. hemionus virus has been genetically transmitted for millions of years and yet has maintained the ability to be expressed as infectious virus, argue for positive evolutionary selective pressures for the maintenance of type C viral genes.

Animals↗
PubMed2026

A Novel Long Noncoding RNA-LNC000133 Associated With Steroid-Induced Osteonecrosis of the Femoral Head Promotes Osteoblast Differentiation Through Bone Marrow Mesenchymal Stem Cells-Derived Exosomes Pathway: A Bioinformatics Validation and Detailed Mechanistic Study.

Steroid-induced osteonecrosis of the femoral head (SONFH) is a debilitating disease caused by glucocorticoid abuse, characterized by complex pathogenesis and unclear molecular mechanisms. Dysfunction of bone marrow mesenchymal stem cells (BMSCs) and their exosome-mediated signalling is a key contributor to SONFH, although the precise mechanisms remain to be elucidated. In this study, the differential expression profiles of long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and messenger RNAs (mRNAs) in exosomes derived from human BMSCs (hBMSCs) obtained from patients with SONFH compared to controls with femoral neck fractures were identified. Through next-generation sequencing, a novel lncRNA, LNC000133, associated with SONFH was discovered. Using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and competing endogenous RNA (ceRNA) network construction, the LNC000133/miR-362-5p/TGF-β3/SMAD3/BMP2 signalling axis was established. The definitive expression, localization and full-length sequence of LNC000133 in BMSCs were subsequently validated by Northern blot, quantitative real-time polymerase chain reaction (qRT-PCR), fluorescence in situ hybridization (FISH) and rapid amplification of cDNA ends (RACE). Most notably, mechanistic studies demonstrated that LNC000133-modified BMSCs-derived exosomes were efficiently taken up by osteoblasts, which promoted proliferation and osteogenic differentiation by targeting the miR-362-5p/TGF-β3/SMAD3/BMP2 signalling pathway.

Humans↗
PubMedDate not supplied

Spontaneous mutation of RNA tumour viruses.

There are 2 categories of spontaneously occurring avian and mammalian RNA tumour virus mutants: conditional and non-conditional. 1) Conditional mutants are able to replicate in or transform cells only under certain physiological conditions or in certain cells. RNA tumour virus temperature-sensitive mutants, focus-morphology mutants, and host range mutants are spontaneously formed. Some of these conditional mutants probably arise by point mutations in the viral genome. 2) Non-conditional mutants have genetic lesions that render them inactive under all conditions. There are non-conditional spontaneous RNA tumour virus mutants that are missing either the virion envelope glycoprotein or both the envelope glycoprotein and the virion DNA polymerase. These mutants cannot replicate or transform cells. Other spontaneous non-conditional mutants can replicate but are defective in their ability to transform fibroblastoid cells. These spontaneous transformation-defective mutants can have deletions in 10-20% of the genomic RNA. Conditional mutants with an altered host range occur at a high rate of approximately 1 mutation/50 infected cell generations during DNA-to-DNA information transfer. This type of conditional mutation requires cell replication but does not occur frequently either during the original synthesis of viral DNA (RNA-to-DNA information transfer) or during the transcription of progeny viral RNA from the (RNA-to-DNA information transfer) or during the transcription of progeny viral RNA from the DNA (DNA-to-RNA information transfer). Temperature-sensitive and focus-morphology mutants also have a high rate of spontaneous formation. Non-conditional mutants missing the viral envelope glycoprotein, DNA polymerase, or transformation gene, also appear to be spontaneously formed at a high rate. Normal avian and mammalian cells contain RNA tumour virus-related genes in their DNA. It is hypothesized that these endogenous RNA tumour virus-related genes in normal cells also have a high rate of spontaneous mutation and are involved in neoplastic processes.

Animals↗
PubMed1981

Alterations in ribonucleic acid synthesis by chromium (III).

The effect of Cr(III) on in vitro RNA synthesis directed by DNA and chromatin isolated from mouse liver was investigated in comparison with other inorganic metals. At 1 mM, CrCl3 significantly stimulated RNA synthesis when incubated with DNA or chromatin prior to the addition of Escherichia coli RNA polymerase, while other metals inhibited it. This stimulation by Cr(III) was caused even at 1 muM CrCl3 on either DNA- or chromatin- directed RNA synthesis. The Cr(III)-complexes of DNA and chromatin also showed significantly enhanced template activities. On the other hand, when RNA polymerase was preincubated with Cr(III), a remarkable inhibition was observed in RNA synthesis directed by both DNA and chromatin. In isolated mouse liver nuclei with endogenous RNA polymerases, Cr(III) stimulated Mg2+-activated RNA synthesis but not Mn2r-(NH4)2SO4-activated synthesis. These results suggest that Cr(III) may alter or regulate gene expressions in mammals.

Animals↗
PubMed1972

Transcription of brain chromatin by ribonucleic acid polymerases from brain nuclei and from Escherichia coli.

1. Transcription of ox brain chromatin by brain nuclear RNA polymerase II and Escherichia coli RNA polymerase was studied. 2. The soluble chromatin prepared from brain nuclei contained DNA, RNA, histone and non-histone proteins. Such chromatin preparations did not display any endogenous RNA polymerase activity, when assayed in the presence of concentrations of KCl as high as 0.4m. 3. The chromatin-templated activity of brain nuclear polymerase II was stimulated by KCl, with an optimum around 0.25m. 4. The template activity of brain chromatin for brain nuclear polymerase II and E. coli enzyme was about 20-25% of that of pure DNA. This greatly repressed templatecapacity of chromatin was probably due to the acid-soluble chromosomal proteins. 5. Brain nuclear polymerase II was 3-4 times more active with dehistonized chromatin than with pure DNA as template, whereas bacterial enzyme was almost equally active with either of these two templates, reflecting the specificity of the transcriptional control mechanisms in mammalian cells.

Animals↗
PubMed1979

The mechanism of decrease in nucleolar RNA synthesis by protein synthesis inhibition.

When protein biosynthesis is inhibited by either cycloheximide of puromycine, the nucleolar RNA synthesis of Ehrlich ascites tumor cells decreases by approximately 70% within 1 h, while the removal of these protein synthesis inhibitors causes a rapid recovery of nucleolar RNA synthesis, largely within 1 h. A similar pattern of decrease and recovery of endogenous RNA polymerase activity in isolated nucleoli or in nuclei (in the presence of alpha-amanitin) may be demonstrated after addition and removal of these drugs. Analysis of the molecular species of RNA polymerase I on a phosphocellulose column indicates that only the IB form of the enzyme decreases in the nucleoli of drug-treated cells and recovers quickly after resumption of protein synthesis. The finding that the activity of the IB form enzyme remains unchanged in the whole nuclei indicates that during cessation of protein synthesis RNA polymerase IB is either released from the nucleoli into the extranucleolar compartment or becomes so loosely bound to the nucleoli that it is leached out from the nucleoli during their isolation. By using a system of assaying free, nucleolar-template bound and total RNA polymerase I activities, data supporting the above interpretation have been obtained. Namely, in isolated nuclei free enzyme activity increases with a concomitant decrease in bound enzyme activity during protein synthesis inhibition, while the total enzyme activity remains unchanged. In isolated nucleoli, both total and bound enzyme activities decreases on protein synthesis inhibition but recover quickly on its resumption. The putative bound enzyme, fractionated with the aid of actinomycin D, is exclusively IB form, whereas the unbound enzyme consists of both IA and IB forms as previously demonstrated (1). No conversion of IB form polymerase to IA form was noted on prolonged sonication in our system. The levels of ATP and GTP in the cell did not change appreciably either during cessation or resumption of protein synthesis in these cells. The data support the previous conclusion that some short-lived protein(s) is required to maintain the normal level of ribosomal RNA transcription (2) and further suggest that the protein is required to facilitate reinitiation of the transcription by RNA polymerase IB in the nucleolus.

Adenosine Triphosphate↗
PubMed1994

Characterization of two classes of ribonucleoprotein complexes possibly involved in RNA editing from Leishmania tarentolae mitochondria.

The molecular mechanism of RNA editing in trypanosomatid mitochondria is an unsolved problem. We show that two classes of ribonucleoprotein complexes exist in a mitochondrial extract from Leishmania tarentolae and appear to be involved in RNA editing. The 'G' class of RNP complexes consists of 170-300 A particles which contain guide RNAs and proteins, show little terminal uridylyl transferase (TUTase) activity and exhibit an in vitro RNA editing-like activity. The 'T' class consists of approximately six RNP complexes, the endogenous RNA of which can be self-labeled with [alpha-32P]UTP. The most abundant T complex, T-IV, is visualized by electron microscopy as 80-140 A particles. This complex exhibits TUTase activity in the native gel and contains guide RNAs. Both G and T complexes are possibly involved with RNA editing in vivo. These results are a starting point for the analysis of the biochemistry of RNA editing.

Animals↗
PubMed1987

Mithramycin selectively inhibits transcription of G-C containing DNA.

Mithramycin induces a reversible inhibition of cellular RNA synthesis without affecting DNA synthesis. The authors have shown this drug induces myeloid differentiation of HL-60 promyelocytic leukemia cells and is an effective agent in certain patients with chronic granulocytic leukemia. In order to investigate the mechanism by which this drug inhibits RNA synthesis we have compared the effect of mithramycin on RNA synthesis by whole cells, isolated nuclei, and RNA synthesis by isolated E. coli RNA polymerase and eukaryotic RNA polymerase II. Exposure of HL-60 cells to mithramycin at concentrations of 4.6 X 10(-7) m or higher for 48 hours causes an almost immediate inhibition of RNA synthesis (up to 85% at 4 hours) with only modest cytotoxicity at these concentrations. Endogenous RNA synthesis by isolated nuclei can be inhibited by mithramycin only at high concentrations (greater than 10(-5) m), suggesting that mithramycin primarily may inhibit initiation, rather than elongation. Mithramycin inhibits in vitro transcription of salmon sperm DNA by E. coli RNA polymerase at DNA:drug ratios similar to those required for RNA synthesis inhibition in whole cells. Similar DNA binding studies with synthetic oligonucleotides demonstrate that mithramycin is a potent inhibitor of transcription of Poly dG.dC by E. coli RNA polymerase but has no effect on transcription of Poly dA.dT. The rapid inhibition of whole cell and isolated RNA polymerase transcription, and the relative insensitivity of isolated nuclei, suggest mithramycin may interact with specific DNA sequences in order to inhibit the initiation of RNA synthesis in intact cells.

Base Composition↗
PubMed2000

Double-stranded RNA interference in Trypanosoma brucei using head-to-head promoters.

The discovery of double-stranded RNA interference (dsRNAi) in Trypanosoma brucei provides a convenient method to generate knockout phenotypes in this protozoan parasite [Ngo H, Tschudi C, Gull K, Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA 1998;95:14687-14692]. The presence of double-stranded RNA (dsRNA) dominantly silences gene expression in a sequence-specific manner by causing the corresponding endogenous RNA to be degraded. To simplify the generation of knockout phenotypes in T. brucei via dsRNAi, we used two promoters arranged as an inverted repeat on a plasmid. This promoter arrangement generates transcripts of both strands of DNA inserted between the promoters, which then form dsRNA. We have used plasmids encoding either two T. brucei ribosomal RNA promoters or two bacteriophage T7 promoters to interfere with expression of alpha-tubulin (TUB), green fluorescent protein (GFP), paraflagellar rod protein A (PFRA), flagellum-adhesion glycoprotein 1 (FLA1), and histone 2B (H2B) in T. brucei. We show here that FLA1 is required for flagellar attachment in T. brucei and that H2B is required for parasite growth. Thus, the two-promoter approach efficiently generates dsRNAi in T. brucei and can be used to produce both specific and random knockout phenotypes in T. brucei. This approach should be useful in generating knockout phenotypes in other kinetoplastid parasites including Trypanosoma cruzi and Leishmania.

Animals↗
PubMed1980

The effect of amino acid starvation on nucleoside uptake and RNA synthesis in Tetrahymena.

The uptake of nucleosides and the synthesis of RNA in Tetrahymena thermophila were examined following amino acid starvation. Omission of leucine, phenylalanine, or arginine from the medium resulted in a rapid decrease in the incorporation of [3H]uridine into the acid-soluble pool and acid-insoluble material (RNA). Amino acid starvation inhibited the uptake of all ribo- and deoxyribonucleosides tested but did not affect the uptake of amino acids or glucose. In addition, under the conditions used, the omission of an amino acid did not result in a large decrease in amino acid incorporation into total protein. Treatment of cells with cycloheximide or emetine gave results similar to the effects of amino acid starvation, but in these experiments the inhibition of protein synthesis was essentially complete. Nucleotide pool sizes were also measured following amino acid starvation. ATP and UTP levels were essentially unchanged, but the dTTP pool size was decreased by 40%. The decrease in RNA synthesis in vivo in the absence of an essential amino acid was reflected in the endogenous RNA synthetic activity of isolated nuclei. However, when solubilized RNA polymerase activity was measured with calf thymus DNA as template, no significant difference was observed between control and amino acid-starved cells.

Amino Acids↗
PubMed1978

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells.

Nuclei were isolated from synchronized HeLa S3 cells and transcribed utilizing their endogenous RNA polymerases. Our data suggest that S phase nuclei are capable of synthesizing histone mRNA sequences while nuclei from G1 phase cells are not. Transcription of histone mRNA sequences by S phase nuclei can be abolished completely by low levels of alpha-amanitin (1.0 microgram/ml, a concentration which completely inhibits RNA polymerase II). From these results it appears that transcription of the histone mRNA sequences occurs during the S phase but not during the G1 phase of the cell cycle and that RNA polymerase II is responsible for histone gene readout.

Amanitins↗
PubMed2005

Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells.

Dynamic analysis of viral nucleic acids in host cells is important for understanding virus-host interaction. By labeling endogenous RNA with molecular beacon, we have realized the direct visualization of viral nucleic acids in living host cells and have studied the dynamic behavior of poliovirus plus-strand RNA. Poliovirus plus-strand RNA was observed to display different distribution patterns in living Vero cells at different post-infection time points. Real-time imaging suggested that the translocation of poliovirus plus-strand RNA is a characteristic rearrangement process requiring intact microtubule network of host cells. Confocal-FRAP measurements showed that 49.4 +/- 3.2% of the poliovirus plus-strand RNA molecules diffused freely (with a D-value of 9.6 +/- 1.6 x 10(-10) cm2/s) within their distribution region, while the remaining (50.5 +/- 2.9%) were almost immobile and moved very slowly only with change of the RNA distribution region. Under the electron microscope, it was found that virus-induced membrane rearrangement is microtubule-associated in poliovirus-infected Vero cells. These results reveal an entrapment and diffusion mechanism for the movement of poliovirus plus-strand RNA in living mammalian cells, and demonstrate that the mechanism is mainly associated with microtubules and virus-induced membrane structures.

Animals↗
PubMed1985

A general method for preparing chromatin containing intact DNA.

A simple and general method is described for preparing chromatin from eukaryotic cells using isotonic conditions. First, cells are encapsulated in agarose microbeads and then lysed using Triton X-100 in the presence of a chelating agent and a physiological concentration of salt. Most cytoplasmic proteins and RNA diffuse rapidly out through pores in the beads to leave encapsulated chromatin which is nevertheless completely accessible to enzymes and other probes. This chromatin can be manipulated freely without aggregation in a variety of different salt and detergent concentrations. It also contains intact DNA since removal of the histones releases superhelical DNA. Conditions are described for incubating this chromatin at 37 degrees C in the presence of Mg2+ ions without any nicking of the DNA. We illustrate the usefulness of this chromatin in investigations on the attachment of nascent RNA to the nucleoskeleton, the accessibility of the ribosomal locus to EcoRI and the properties of the endogenous RNA polymerase II. This type of chromatin preparation should prove useful for both structural and functional studies.

Cell Nucleus↗
PubMed1978

Control of ribosomal RNA synthesis in Escherichia coli. IV. Frequency of transcription of ribosomal RNA genes as a function of growth rate.

Nucleoids were isolated from Escherichia coli B/r cells in steady-stage growth at different rates. The number of RNA chains growing on each nucleoid was estimated from the amount and size of RNAs synthesized by endogenous RNA polymerase. This figure represents the number of RNA polymerase molecules that are functioning in transcription and thus serves to indicate the frequency of transcription in the cells. With an increase in the growth rate from 0.27 to 1.73 (h-1), (a) the number of total RNA chains per genome increases from about 252 to 838, (b) the number of ribosomal RNA (rRNA) chains per genome increases as a function of the second power of the growth rate from about 19 to 255, and (c) the number of non-rRNA chains per genome increases linearly from about 233 to 538.

DNA-Directed RNA Polymerases↗
PubMed1974

Poly(A) polymerase from vaccinia virus-infected cells. I. Partial purification and characterization.

Poly(A) polymerase activity is induced during vaccinia virus infection of HeLa cells. The enzyme is maximally induced at 3.5 h postinfection. Partial purification frees the preparation of RNase activity and RNA polymerase activity. ATP is the substrate for poly(A) synthesis. A small amount of poly(A) is produced from added adenosine diphosphate due to the production of ATP by an adenylate kinase present in the preparation. The incorporation of ATP into poly(A) is dependent on divalent cations (Mg(2+) or Mn(2+)) and is not inhibited by UTP, CTP, or GTP. Poly(U) stimulates ATP incorporation; poly(A) and poly(C) have little effect on ATP incorporation, and poly(dT) is extremely inhibitory. RNA prepared from HeLa cells and from the partially purified poly(A) polymerase (the enzyme preparation contains endogenous RNA [Brakel and Kates]) stimulates ATP incorporation by poly(A) polymerase which was subjected to DEAE-cellulose chromatography. RNase's, pancreatic and T(1), inhibit the production of poly(A). DNase has little effect. Poly(U) is able to stimulate poly(A) production in the presence of T(1) RNase.

Adenine Nucleotides↗
PubMed1981

Inhibition of tubulinyl-tyrosine carboxypeptidase by brain soluble RNA and proteoglycan.

Rat brain extracts contain two heat-stable, nondialyzable inhibitors of tubulinyl-tyrosine carboxypeptidase. One of the inhibitors was sensitive to ribonuclease and insensitive to trypsin and pronase, indicating that the inhibitor is RNA. This is supported by the observation that purified RNA from rat brain inhibited the enzyme activity to the same extent as similar amounts of the endogenous RNA. Similar results were obtained with calf liver RNA. The other inhibitor was purified by chromatography on a DEAE-Sephadex and identified as proteoglycan. The elimination of the protein moiety of the proteoglycan resulted in a small increase of its inhibitory activity. Glycosaminoglycan was released from the proteoglycan by beta elimination, indicating that the linkage between glycosaminoglycan and the protein moiety is through an O-glycosidic bond. The glycosaminoglycan contains uronic acid, hexosamine and sulfate in a molar ratio of 1:1.01:0.99, respectively. Treatment of the glycosaminoglycan with chondroitinase ABC completely abolished its inhibitory activity. Chondroitin sulfate A, chondroitin sulfate B, chondroitin sulfate C, and the brain glycosaminoglycan inhibited tubulinyl-tyrosine carboxypeptidase to the same extent when used in comparable amounts.

Animals↗