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Results for “RNA Aggregation”

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At least 19 recordsLinked to original sources
PubMed1977

RNA aggregation during sulfhydryl-agarose chromatography of mercurated RNA.

Isolation of newly synthesized mercurated RNA transcripts by chromatography on sulfhydryl-agarose has recently been used to reduce contamination by endogenous RNA derived from the chromatin template. We show that substantial RNA aggregation occurs during standard isolation procedures, causing significant retention of endogenous (unmercurated) RNA on sulfhydryl-agarose. We describe methods to reduce substantially this problem and discuss the implications of our findings for interpretation of previous hybridization and transcription experiments.

Animals↗
PubMed1975

Isolation of RNA transcripts from the entire Sendai viral genome.

Three classes of viral transcripts (18S, 24S, and 33S) were isolated from viral ribonucleoproteins in Sendai virus-infected cells. Hybridization studies with virion minus strand genome RNA demonstrated that the 18S RNA contained transcripts from 60% of the viral genome while the 33S RNA contained transcripts from the entire viral genome. Brief heat of ME2SO treatment of the 33S RNA demonstrated that this RNA was composed of two classes: RNA which continued to sediment at 33S (33S RNA) and 18S RNA aggregates (18S RNA). The 33S RNA was determined to be a transcript from the 40% of the viral genome not protected by the 18S RNA. The aggregated 18S RNA does not appear to be an artifact of isolation.

Culture Techniques↗
PubMed1977

Frog oocytes synthesize and completely process the precursor polypeptide to virion structural proteins after microinjection of avian myeloblastosis virus RNA.

After microinjection of Xenopus laevis oocytes with RNA from avian myeloblastosis virus, viral structural proteins p27, p19, p15, and p12 are formed by a sequence of posttranslational cleavages of a high-molecular-weight precursor polypeptide. The 60-70S RNA aggregate or its 30-40S RNA subunits obtained by heat or formamide treatment possess the same ability to serve as template in X. laevis oocytes. The processing pattern of virus-specific precursor polypeptides is the same in X. laevis oocytes as in chick embryo fibroblasts infected with avian myeloblastosis virus, but the processing takes place at a much slower rate.

Animals↗
PubMed1976

[Isolation of RNA containing a polyadenylic acid sequence by chromatography on unmodified cellulose].

A new modification of the procedure of the isolation of polyA-containing RNAs is worked out, which makes possible to isolate this RNA fraction free of considerable contamination with rRNA. The administration of 0.0001 M EDTA-Na2 provides the absence of RNA aggregation and prevents non-specific RNA binding on cellulose columns, which takes place when more high EDTA-Na2 concentrations in elution solutions are applied. Under these conditions synthetic polyA in model experiments practically completely binds with cellulose in a broad range of concentrations. It permits to use the procedure described for the preparative isolation of RNA fractions, containing polyA sequences.

Animals↗
PubMed1976

Molecular model for 5-S RNA. A small-angle x-ray scattering study of native, denatured and aggregated 5-S RNA from Escherichia coli ribosomes.

A tertiary structural model is suggested for Escherichia coli 5-S RNA that consists of one large and two small double helices arranged in the form of the letter Y. This model is consistent with the small-angle X-ray scattering data of native 5-S RNA, measured in the angular range 20 less than or equal to 140 mrad. The radium of gyration is 3.61 +- 0.1 Nm. Denatured 5-S RNA yields a much lower radius of gyration, 2.7 nm, which might indicate that during denaturation one minor double-helical arm of the Y-shaped structure partially collapses into single-stranded areas. At high concentrations (60 mg/ml) of 5-S RNA, the X-ray scattering data indicate that 5-S RNA is aggregated.

Base Sequence↗
PubMed1975

RNA polymerase stimulation: effect of aldosterone and other adrenocorticoids on RNA turnover in rat kidney.

The results of steroid hormone stimulation of aggregate RNA polymerase ?activity in kidney can be interpreted in terms of either template or enzyme alterations. In order to discover the effect of aldosterone on enzyme or DNA template, the RNA polymerases were purified from kidney nuclei of normal, adrenalectomized or adrenalectomized plus aldosterone treated rats and the activity was determined using different sources of DNA. It was found that the DNA from aldosterone treated rats was transcribed more efficiently than from other sources. Aldosterone does not seem to have a direct effect on the RNA polymerase. Fractionation of ([14-C]aldosterone injected) kidney chromatin revealed the presence of radioactivity in the non-histone acidic proteins and DNA, suggesting the possible binding of aldosterone or aldosterone-receptor complex to these chromatin fractions which may result in enhanced template activity. Turnover of RNA was also studied in various subcellular fractions: nuclei, mitochondria, rough endoplasmic reticulum, smooth endoplasmic reticulum, polysomes, ribosomes and sRNA, in normal, adrenalectomized, and adrenalectomized plus adrenocortical hormone treated rat kidney, by following the loss of radioactivity after a single injection of [14-C]-orotic acid. Daily administration of aldosterone or deoxycorticosterone reversed the effects of adrenalectomy. Daily administration of corticosterone was without effect.

Adrenal Glands↗
PubMed1978

Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone.

Recipient strains of Streptococcus faecalis produce a trypsin sensitive, heat resistant, nuclease resistant factor, designated clumping-inducing agent (CIA) which causes strains carrying certain conjugative plasmids to aggregate. RNA and protein synthesis but not DNA synthesis are required for aggregation to occur. Recipient filtrates that contain CIA activity also induce donors to mate at high frequencies. Introduction of a transferable plasmid into strains producing CIA dramatically reduces the amount of CIA activity produced by the strain but allows the strain to respond to exogenously added CIA. Our data suggest that CIA represents a bacterial sex hormone (pheromone).

Animals↗
PubMed1978

Basophil histamine release by RNA, DNA and aggregated IgG examined in rheumatoid arthritis and systemic lupus erythematosus. Results compared with basophil counts and antinuclear antibodies.

Basophils from patients with rheumatoid arthritis (RA) respond to RNA, DNA and immune complexes (aggregated IgG) with histamine release. The RNA response was well correlated to the clinical activity of the disease, since histamine liberation was found in all patients with severe activity, whereas no liberation was observed in patients with moderate or quiescent activity. A less significant correlation was obtained with DNA and aggregated IgG. In contrast, no response was obtained with RNA, DNA and aggregated IgG in patients with systemic lupus erythematosus (SLE) or in controls. In the RA and the SLE groups no significant correlation was found between the response of RNA, DNA and aggregated IgG and the serum titres of anti-DNA and antinuclear antibodies. No difference in basophil cell count in peripheral blood and basophil histamine content was found between RA, SLE and controls. Our results point to an involvement of an autoimmune type I reaction in the pathogenesis of RA directed against the nuclear components RNA and DNA and against immune complexes.

Adolescent↗
PubMed1976

Poly(A)-containing RNA in Tetrahymena pyriformis.

Poly(A)-containing RNAs with sedimentation coefficients in the range 10-45 S and 10-35 S (Mr 0.2-3.3 x 10(6) and 0.2-2.2 x 10(6) approximately) are present in the nucleus and cytoplasm of T. pyriformis respectively. The poly(A) segments present in both nuclear and cytoplasmic poly(A)-containing RNAs have a chain length of 80 - 150 nucleotides. Significant amounts of high-molecular-weight poly(A)-containing RNAs (35 S, Mr 2.2 x 10(6) are found in the post-polysomal fraction of the cytoplasm (messenger ribonucleoprotein particles?) and also in large polysomes. In order to exclude the possibility that these high-molecular-weight species are products of non-specific aggregation, RNA preparations were submitted to severe denaturing conditions before analysis and all electrophoreses were carried out in the presence of 95% (v/v) formamide.

Animals↗
PubMed2026

Nuclear export modulates TDP-43 phase transition and cytoplasmic aggregation.

RNA-binding protein TAR DNA-binding protein 43 (TDP-43) can form liquid-like, nuclear assemblies whose phase behavior may influence its aggregation propensity and neurotoxic activity. The mechanism(s) that modulates the transition of TDP-43 from a liquid to solid phase is poorly defined. Here we combine chemical and genome-wide genetic screenings to identify cellular factors that modulate the phase behavior of an RNA-binding defective TDP-43 mutant that mimics an Amyotrophic Lateral Sclerosis (ALS)-associated variant. Our screens uncover multiple cellular processes including RNA splicing, protein translation, proteostasis imbalance and nuclear export as TDP-43 phase regulators. Importantly, TDP-43 phase transition can be dynamically recapitulated in vitro in a semi-permeabilized cell system, which reveals that the inhibition of nuclear export reshapes the nuclear environment in favor of an RNA-dependent TDP-43 liquid-liquid phase separation (LLPS) state, which mitigates cytoplasmic TDP-43 aggregation. We validated this mechanism in a brain organoid model bearing an ALS-associated mutation, showing that nuclear export deficiency can limit pathogenic phospho-TDP-43 accumulation. These findings establish nuclear export as a key regulator of TDP-43 phase transitions and define a mechanistic framework that links altered nuclear transport and phase dynamics to TDP-43 aggregation potential.

Amyotrophic Lateral Sclerosis (ALS)↗
PubMed2026

Cellular modifiers of TDP-43 phase transition and cytoplasmic aggregation.

RNA-binding protein TAR DNA-binding protein 43 (TDP-43) can form liquid-like nuclear assemblies whose phase behavior is thought to influence its aggregation propensity and neurotoxic activity. The mechanisms that govern the liquid-to-solid phase transition of TDP-43 remain poorly defined. Here, we combined chemical and genome-wide genetic screens to identify cellular factors that modulate the phase behavior of an RNA-binding-defective TDP-43 mutant. Our screens uncovered multiple cellular processes, including RNA splicing, protein translation, proteostasis imbalance, and nuclear export as TDP-43 phase regulators. We also developed a semi-permeabilized cell system that partially recapitulates the TDP-43 phase transition in vitro, and showed that nuclear export inhibition reshapes the nuclear environment to favor RNA-dependent liquid-liquid phase separation (LLPS) of TDP-43, which mitigates its aggregation. Nuclear export inhibition in a brain organoid model bearing an ALS-associated mutation reduces pathogenic phospho-TDP-43 accumulation. These findings identify multiple modulators of TDP-43 phase transitions in a sensitized model system and establish a framework for further dissecting the link between nuclear transport and TDP-43 phase dynamics.

DNA-Binding Proteins↗
PubMed1991

Thermal stability of turnip yellow mosaic virus RNA: effect of pH and multivalent cations on RNA deaggregation and degradation.

Light scattering studies of RNA isolated from turnip yellow mosaic virus (TYMV) revealed a molar mass of 1.9.10(6) g mol-1, which is close to the value of 2.0.10(6) g mol-1 published for intact genomic TYMV RNA (2M RNA). However, gel electrophoresis under denaturing conditions demonstrated that only 30-40% of this native RNA was 2M RNA. Sucrose gradient centrifugation revealed the occurrence of a series of smaller RNA size classes, the mass ratios of which were greatly influenced by the pH of the solution and the presence of EDTA. These results suggest that native TYMV RNA preparations originally contain a mixture of intact RNA particles and of aggregates of RNA fragments with the same molar mass of about 2.10(6) g mol-1, and that the size classes are intermediates in the deaggregation process of the degraded genomic TYMV RNA. The native RNA displayed pH-dependent deaggregation and degradation. The degradation process of 2M RNA followed (pseudo) first-order kinetics. Lower degradation rates were observed for RNA depleted of divalent cations and polyamines. For depleted 2M RNA an enthalpy of activation of about 100 kJ mol-1 and an almost zero entropy of activation was calculated. Similar values were also found for depleted E. coli ribosomal RNAs and depleted MS2 RNA, demonstrating that all RNAs are equally vulnerable to degradation. In the presence of multivalent cations the activation enthalpy for 2M TYMV RNA degradation increased to 150 kJ mol-1 and the entropy of activation to 150 J K-1 mol-1, indicative for a different degradation mechanism.

Cations, Divalent↗
PubMed1976

Stepwise transition of aggregate structure of high-molecular-weight avian myeloblastosis virus RNA. Mode of releasing of associated 4S RNA.

Mode of releasing of associated 4S RNA species was studied during a controlled transition of aggregate structure of high-molecular-weight AMV-RNA. It has been found that associated 4S RNA constitutes 2.5% of 60S AMV-RNA complex. Approximately 60% of associated 4S RNA is successively released during treatment of viral RNA with increasing formamide concentration, concomitantly with the transition of 60S RNA aggregate through 50--55S RNA intermediate into the final 30--40S RNA subunits. 40% of 4S RNA remains associated with 30--40S RNA subunits prepared by formamide treatment and can be released from them by heating. A procedure is thus provided both for the isolation of oncornaviral RNA subunit structures deprived of various partions of associated 4S RNA and for the fractionation of 4S RNA species according to their binding affinity to the genome oncornaviral RNA.

Avian Leukosis Virus↗
PubMed1976

Subcellular distribution and properties of poly(A)-containing RNA from cultured plant cells.

Cultured sycamore cells rapidly incorporate [3H]uridine or [32P]orthophosphate into rRNA precursors and polydisperse RNA. Mature rRNA accumulates only after a lag period of approximately 40 min. Fractionation of pulse-labelled cells and analysis of the RNA shows that after 30 min the rRNA precursors, together with some polydisperse RNA, are confined to the nucleus. In consequence radioactive polydisperse RNA can be isolated from polyribosomes in the complete absence of labelled rRNA. Approximately 40% of this RNA is retained by an oligo(dT)-cellulose column and by this criterion is judged to contain poly(A) sequences. A smaller proportion of nuclear polydisperse RNA also contains poly(A). The tendency for poly(A)-containing RNA to aggregate complicates molecular weight determinations. Denaturation of poly(A)-containing RNA in 8 M urea prior to gel electrophoresis produces a broad peak of RNA with an average Mr = 10(6). Analysis of the nucleotide composition of total cell poly(A)-containing RNA shows that it contains 41% AMP. Roughly 6% of this RNA is resistant to digestion by ribonuclease A and T1. AMP is the only nucleotide detectable in these fragments. From their mobility during electrophoresis in 8 M urea at 60 degrees C with 5.8-S, 5-S and tRNA as molecular weight markers it is concluded that the poly(A) regions contain an average of 160 nucleotides.

Cells, Cultured↗
PubMed1976

Hybridization of mRNA from adenovirus-transformed cells to segments of the adenovirus genome.

Cytoplasmic viral-specific RNA from the 8617 line of adenovirus type 2 (Ad2) transformed rat cells was hybridized to DNA fragments derived either by Eco-RI or Sma-I restriction endonucleases. Three discrete classes of viral RNA (26S, 20S, and 15S) were detected by hybridization of total cytoplasmic RNA with the fragment, and all of these RNA molecules also hybridized to the much smaller Sma-E fragment of Ad2 DNA. Poly (A)-containing RNA (exposed to 90% formamide) contained only the 20S and 15S mRNA species, suggesting that the 26S RNA might be an aggregated species. Viral RNA of the same size derived from the same regions of the genome has not been detected in lytically infected cells, suggesting some change in the pattern of transcription or RNA processing of the Ad2 DNA in the integrated state.

Adenoviridae↗
PubMed1990

[The mechanism of the proaggregant action on the thrombocytes of RNA and DNA molecules].

The entrance of extracellular Ca2+ in ADP-stimulated human platelets and phospholipase A2 activity have been studied under the action of Ca precipitates DNA, RNA and dsRNA. The nucleic acids and its Ca complexes (Ca-NA) have been found to induce the aggregation of isolated human platelets by stimulation of extracellular Ca2+ entrance into the platelets and the formation of phosphatidilcholine and phosphatidilethanolamine lysoderivatives having the membranolytic effect.

Adenosine Diphosphate↗