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Results for “endogenous RNA”

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At least 55 records · Page 3Linked to original sources
PubMed1979

Transcription of cloned Xenopus 5S RNA genes by X. laevis RNA polymerase III in reconstituted systems.

When incubated with a soluble extract from large oocytes of Xenopus laevis, recombinant DNA plasmids containing either X. laevis oocyte 5S DNA or X. borealis oocyte 5S DNA direct the synthesis of discrete 5S RNAs, which by size and sequence analysis are similar or identical to the corresponding 5S RNAs synthesized in vivo. Synthesis of the 5S RNAs is mediated by a soluble endogenous RNA polymerase III (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6), which presumably recognizes specific initiation and termination sites in the 5S genes. Optimal conditions for accurate synthesis and the kinetics of the reactions have been determined. A soluble postchromatin supernatant fraction has also been isolated from immature oocytes. Although devoid of a functional endogenous RNA polymerase III, this extract contains a component(s) that effects the accurate transcription of 5S genes (in a plasmid) by a purified RNA polymerase III.

Animals↗
PubMed1979

Termination of transcription in nucleoli isolated from Tetrahymena.

Correct termination of transcription of the rRNA gene in nucleoli isolated from Tetrahymena is dependent on a protein factor with a molecular weight between 50,000 and 100,000. At low ionic strength the endogenous RNA polymerase synthesizes a transcript identical in size to the precursor rRNA extracted from cells. In the presence of ammonium sulfate, however, the RNA polymerase reads through the normal termination point as demonstrated by size and hybridization studies of the transcript. After ammonium sulfate treatment, rDNA associated with chromosomal proteins (r-chromatin) can be separated from the termination factor by differential centrifugation. The endogenous RNA polymerase on the salt-treated r-chromatin is no longer able to recognize the normal terminator even at low ionic strength. Normal termination properties can be reconstituted by complementation with intact nucleoli or with a protein factor extracted from nucleoli.

Animals↗
PubMedDate not supplied

[Effect of cyclic-3',5'-AMP on rat liver polynucleotide phosphorylase activity].

Effect of cAMP on the activity of polynucleotide phosphorylase (PNPase) was studied in polyribosome fraction of rat liver tissue. Intraperitonel administration of cAMP or of theophilline into rats distinctly decreased the PNPase activity in the polyribosome fraction. The cAMP (1-10(-4) M) inhibited the enzymatic activity only by 8% in polyribosome fraction in vitro, as it was estimated by the reaction of phosphorolysis of endogenous RNA and polyA added. Any attempts were proved to be uncucessful to reveal cAMP, ATP-dependent proteinkinase in rat liver, responsible for the decrease in the PNPase activity in the polyribosome fraction. The cAMP inhibited the increase in the PNPase activity, coupled with protein biosynthesis in polyribosomes. Moreover, cAMP caused a decrease in the PNPase activity in reaction of polyA phosphorolysis and did not affect the rate of endogenous RNA phosphorolysis in polyribosome fraction, isolated from postmitochondrial fraction after incubation for 15 min at 30 degrees. The 3',5'-cyclo AMP (2-10(-6)-2-10(-4) M) stimulated incorporation of 14C-leucine into acid-insoluble material, when postmitochondrial fraction was incubated under the same conditions. The data obtained suggest that cAMP either inhibits specifically the PNPase synthesis or represses the coupled with protein biosynthesis formation of active "heavy" type of PNPase from less active "light" type.

Animals↗
PubMed1979

Poliovirus polyuridylic acid polymerase and RNA replicase have the same viral polypeptide.

A poliovirus-specific polyuridylic acid [poly(U)] polymerase that copies a polyadenylic acid template complexed to an oligouridylic acid primer was isolated from the membrane fraction of infected HeLa cells and was found to sediment at 4 to 5S on a linear 5 to 20% glycerol gradient. When the poly(U) polymerase was isolated from cells labeled with [(35)S]methionine and was analyzed by glycerol gradient centrifugation and polyacrylamide gel electrophoresis, the position of only one viral protein was found to correlate with the location of enzyme activity. This protein had an apparent molecular weight of 62,500 based on its electrophoretic mobility relative to that of several molecular weight standards and was designated p63. When the poly(U) polymerase was isolated from the soluble fraction of a cytoplasmic extract, the activity was found to sediment at about 7S. In this case, however, both p63 and NCVP2 (77,000-dalton precursor of p63) cosedimented with the 7S activity peak. When the 7S polymerase activity was purified by phosphocellulose chromatography, both p63 and NCVP2 were found to co-chromatograph with poly(U) polymerase activity. The poliovirus replicase complexed with its endogenous RNA template was isolated from infected cells labeled with [(35)S]methionine and was centrifuged through a linear 15 to 30% glycerol gradient. The major viral polypeptide component in a 26S peak of replicase activity was p63, but small amounts of other poliovirus proteins were also present. When the replicase-template complex was treated with RNase T1 before centrifugation, a single peak of activity was found that sedimented at 20S and contained only labeled p63. Thus, p63 was found to be the only viral polypeptide in the replicase bound to its endogenous RNA template, and appears to be active as a poly(U) polymerase either as a monomer protein or as a 7S complex.

Centrifugation, Density Gradient↗
PubMed2026

ceRNA network of lncRNAs and mRNAs in OSF-to-OSCC progression: Diagnostic biomarkers and functional pathways.

BACKGROUND: Oral submucous fibrosis (OSF) is a chronic potentially malignant disorder that can progress to oral squamous cell carcinoma (OSCC). Although dysregulated non-coding RNAs have been implicated in oral carcinogenesis, the competing endogenous RNA (ceRNA)-mediated regulatory mechanisms underlying OSF-to-OSCC progression remain poorly understood. This study aimed to identify candidate regulatory molecules and construct a putative lncRNA-miRNA-mRNA network associated with malignant transformation. METHODS: Publicly available microarray datasets (GSE117973 and GSE125866) were analyzed to identify differentially expressed genes between OSF and OSCC. Differentially expressed transcripts were classified into mRNAs and lncRNAs based on public transcript annotations. Highly correlated lncRNA-mRNA pairs were identified using Pearson correlation analysis and integrated with multiMiR-supported miRNA-mRNA interactions obtained from public databases to construct a putative ceRNA regulatory network. Functional characterization focused on apoptosis, epithelial-mesenchymal transition (EMT), and immune checkpoint-related pathways. Receiver operating characteristic (ROC) analysis was performed to evaluate diagnostic performance, and selected biomarkers were externally validated using The Cancer Genome Atlas (TCGA) OSCC cohort. RESULTS: Integrated transcriptomic analysis identified several dysregulated mRNAs and lncRNAs associated with OSF-to-OSCC progression. Network analysis highlighted TBC1D3B, RREB1, TEAD3, SREBF1, TMEM41B, FOXK2, and KIAA1958 as prominent hub genes within the putative regulatory network. Functional analyses demonstrated significant associations with apoptosis-, EMT-, and immune checkpoint-related genes, suggesting potential involvement in multiple biological processes contributing to malignant transformation. Several hub genes exhibited strong diagnostic performance, with ROC analysis yielding AUC values ranging from 0.891 to 1.000, indicating excellent discrimination between OSF and OSCC samples. External validation using TCGA further supported the relevance of the identified biomarkers in OSCC. CONCLUSIONS: This study provides a comprehensive transcriptomic framework describing putative lncRNA-miRNA-mRNA regulatory interactions associated with OSF progression to OSCC. The identified hub genes and regulatory networks represent candidate biomarkers for early detection and provide a foundation for future mechanistic and experimental validation. As the proposed ceRNA interactions are computationally inferred, further biological validation is required before clinical application.

RNA, Long Noncoding↗
PubMed2026

Construction of circRNA-miRNA-mRNA regulatory networks in the intestine of turbot (Scophthalmus maximus) following Vibrio anguillarum infection.

Circular RNAs (circRNAs) play pivotal roles in post-transcriptional regulation by acting as molecular sponges for microRNAs (miRNAs) within the competitive endogenous RNA (ceRNA) network. However, the regulatory mechanisms in teleost immune responses remain poorly understood. In this study, circRNA-miRNA-mRNA networks were investigated in turbot (Scophthalmus maximus) following Vibrio anguillarum infection to elucidate host-pathogen interactions. Through high-throughput sequencing of intestinal tissues, a total of 50 differentially expressed circRNAs (DE-circRNAs) (18 at 2 hpi, 16 at 12 hpi, 16 at 48 hpi), 212 DE-miRNAs (11 at 2 hpi, 70 at 12 hpi, 15 at 48 hpi), and 1774 DE-mRNAs were identified. Functional enrichment analyses (GO/KEGG) revealed significant associations with immune pathways, including the MAPK signaling pathway and gap junction. An integrated circRNA-miRNA-mRNA regulatory network was constructed, highlighting key interactions including novel_circ_0002573/DE-miR-27a-3p/FGB and novel_circ_0002423/novel_347/GNE, which may regulate inflammatory and antibacterial responses. The expression patterns of selected circRNAs, miRNAs and mRNAs were validated using qRT-PCR, confirming the reliability of the sequencing results. Importantly, fibrinogen beta chain (FGB) and CXCR4/CXCL12 signaling were identified as critical immune modulators. These findings provide insights of the ceRNA regulatory networks involved in teleost intestinal immunity and provide potential molecular targets for selective breeding of disease resistance in this species.

Animals↗
PubMed1977

Selective and accurate transcription of the Xenopus laevis 5S RNA genes in isolated chromatin by purified RNA polymerase III.

Chromatin isolated from immature oocytes was found to contain an endogenous RNA polymerase activity (RNA nucleotidyltransferase; nucleoside triphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) that synthesizes predominately 5S RNA. However, the levels of total RNA synthesis and 5S RNA synthesis in chromatin were each stimulated 10- to 50-fold by an exogenous RNA polymerase III purified from X. laevis oocytes. The 5S genes in chromatin were transcribed by the exogenous enzyme in a highly selective (3000-fold above random) and predominately asymmetric fashion. A significant fraction of 5S RNA sequences were also found in a discrete transcript, approximately 5S in size. Total RNA synthesis was significantly stimulated when chromatin was transcribed by oocyte RNA polymerase I, murine RNA polymerase II, and low levels of Escherichia coli RNA polymerase. However, these enzymes did not significantly stimulate 5S RNA synthesis above the endogenous levels. Both homologous oocyte RNA polymerase I and III and E. coli RNA polymerase transcribed the 5S genes in deproteinized DNA to approximately the same extent (severalfold above random) and both the sense and anti-sense strands of the gene were transcribed. It appears, therefore, that both chromatin-associated components and a purified RNA polymerase III are necessary and sufficient for the selective and accurate transcription of the 5S RNA genes in vitro.

Animals↗
PubMed1976

Effect of Sarkosyl on chromatin and viral RNA synthesis. The isolation of SV40 transcription complex.

The endogenous RNA polymerase activity of mouse nucleic is enhanced several-fold by the anionic detergent Sarkosyl. The action of Sarkosyl is exerted primarily on the alpha-amanitin sensitive form of the enzyme. This detergent causes the release of nearly all the protein associated with cellular DNA but does not release initiated RNA polymerase. Sarkosyl was also able to activate the RNA polymerase activity from mitotic cells, in which transcription of the highly condensed chromatin is minimal. The use of this anionic detergent has also permitted the extraction of a nucleoprotein complex from Simian Virus 40 (SV40) infected monkey cells. Molecular hybridization experiments have established the viral specificity of the RNA synthesized in vitro by the endogenous polymerase present in this complex.

Animals↗
PubMed1977

Phage T4-modified RNA polymerase transcribes T4 late genes in vitro.

Initiation of T4 late RNA synthesis has been achieved in an in vitro system prepared from Escherichia coli cells infected with wild-type or maturation-defective mutant T4 phage. The system uses a cellophane membrane as a mechanical support for concentrated cell lysates and for added streptolydigin-resistant RNA polymerases. Transcriptional activity and selectivity of added RNA polymerases are tested while endogenous RNA polymerase activity is inhibited by streptolydigin. T4-modified RNA polymerase is required for substantial stimulation of T4 late RNA synthesis.

Coliphages↗
PubMed1979

The specificity of in vitro chromatin transcription.

The in vitro transcription of chicken reticulocyte chromatin with E. coli RNA polymerase has been studied in several different ways. The amount of globin RNA sequences has been measured by hybridizing the transcript with globin cDNA; we show that under the proper conditions mercurated transcript RNA can be separated from endogenous RNA on sulfhydryl affinity columns. The amount of globin RNA in the transcript is approximately 20 fold greater than that from erythrocyte chromatin or reticulocyte DNA. Although these data could be used to support the hypothesis of specific transcription, we show by RNA/RNA self hybridization of the transcript (which is at least 50% symmetric) and by hybridization of the transcript to unique DNA in vast RNA excess that the bulk of the chromatin transcript differs little from the transcript of naked DNA. Several explanations for these apparently contradictory results are offered with the most likely one being compatible with random transcription of at least most of the sequences in the chromatin.

Animals↗
PubMed1979

Isolation of a minichromosome containing the ribosomal genes from Physarum polycephalum.

The ribosomal genes of Physarum polycephalum are located on linear DNA molecules (rDNA) of 38 x 10(6) daltons present in each nucleolus in 100--200 copies. The rDNA is not part of the large chromosomal DNA. These molecules have now been solubilized in the form of transcriptionally active deoxyribonucleoprotein complexes from nucleoli purified through Percoll gradients. The ribosomal chromatin (rDNP) sediments in sucrose gradients as a homogeneous fraction with an approximate sedimentation coefficient of 100 S. It contains alpha-amanitin-resistant RNA polymerase I activity and rDNA as its major (or sole) DNA component. Buoyant density analysis indicates that ribosomal chromatin contains, besides RNA polymerase I, significant amounts of additional protein. RNA synthesized in vitro by the endogenous RNA polymerase is complementary to rDNA and is transcribed mainly from the sequences coding for 19S and 26S ribosomal RNA.

Amanitins↗
PubMed1975

Nuclear receptors for thyroid hormone: evidence for nonrandom distribution within chromatin.

Chromatin receptor proteins appear to mediate some actions of thyroid hormone. In this study, sheared mammalian chromatin containing [125I]triiodothyronine (T3) bound by these receptors was separated using sucrose gradient velocity sedimentation. T3-receptor complexes were distributed throughout the chromatin fractions, but were enriched in the slowly sedimenting fractions. The latter contain most of the template capacity for RNA synthesis and most of the endogenous RNA polymerase activity but a minor portion of the total DNA. Formaldehyde treatment of chromatin containing receptor-bound [125 I ]T3 resulted in fixation of radioactivity, as evidenced by its migration with chromatin after equilibrium density gradient sedimentation in both cesium chloride and Conray. This fixation implies that the T3 receptor protein is closely associated with chromatin. These results suggest that proteins involved in the regulation of gene function may be nonrandomly distributed within chromatin subfractions, and are consistent with a direct role for thyroid hormone in regulating genetic expression.

Animals↗
PubMed1976

Effects of adriamycin on the reverse transcriptase and the production of murine leukemia virus.

Adriamycin inhibited the endogenous RNA-, poly (A)-d(T)12-, and calf thymus DNA-catalyzed reaction of reverse transcriptase from AKR mouse murine leukemia virus (AKR-MLV). This inhibition was found at the reaction levels of endogenous RNA-directed and subsequent DNA-directed DNA synthesis. Although adriamycin and actinomycin D significantly reduced the growth of AKR mouse cells (K3b), the treatment with adriamycin could bot inhibit the AKR-MLV production in these cells. Actinomycin D inhibited AKR-MLV production completely in the same experimental condition. In adriamycin-resistant K3b/Am cells, which were isolated by intermittent treatment of K3b cells with adriamycin, persistence of AKR-MLV was demonstrated. K3b/Am cells showed some altered characteristics such as reduced growth rate and tumorigenicity.

Animals↗
PubMed2026

CRISPR/Cas- and Argonaute-Based In Vivo Nucleic-Acid Imaging Technologies: Strategies, Challenges, and Perspectives.

Live-cell monitoring of sequence-specific nucleic acids is essential to understanding genome organization, RNA regulation, and disease progression. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) and Argonaute (Ago) systems provide programmable, guide-directed recognition of DNA or RNA and are increasingly used as platforms for in vivo bioimaging. This review summarizes the structural and mechanistic features of representative CRISPR and Ago effectors and discusses design strategies for sensitive, specific, and multiplexed imaging of genomic loci, extrachromosomal DNA, and endogenous RNA in living cells. We compare the analytical performance and limitations of CRISPR- and Ago-based imaging, with particular emphasis on the major technical and biological challenges affecting their accuracy, applicability, and reliability. Finally, this review offers insights into developing high-resolution and user-friendly bioimaging platforms for fundamental biology and future translational applications.

CRISPR↗
PubMed1976

Fidelity of chromatin transcription in vitro.

Chromatin and DNA from Schneider's Drosophila melanogaster cell line 2 were transcribed in vitro with Escherichia coli RNA polymerase. Using mercurated UTP as precursor, the newly synthesized RNA could be separated from DNA and endogenous RNA by affinity chromatography on sulfhydryl-Sepharose 6B. Characterization of the transcription products with complementary DNA (cDNA) made from polyadenylated nuclear RNA and with fractionated cDNA probe demonstrated a fair quantitative fidelity in the in vitro transcript from chromatin which was not evident when DNA was transcribed. However, as shown by hybridization to total nuclear RNA, E. coli RNA polymerase transcribed both DNA strands from chromatin in vitro. We conclude that E. coli polymerase is able to distinguish sections of chromatin at which rapid synthesis of RNA occurs in the cell.

Cell Line↗