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Results for “RNA, Small Cytoplasmic”

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PubMed1986

Localization of Epstein-Barr virus-encoded small RNAs by in situ hybridization.

Human B lymphocytes latently infected with Epstein-Barr virus (EBV) synthesize two low molecular weight RNAs designated EBER 1 and 2. Using an in situ hybridization technique we have localized EBER 1 and 2 within the nucleus of single EBV-harboring B lymphocytes from established and recently transformed cell lines. As controls, the locations of the small nuclear RNA, U1, and the small cytoplasmic RNA, 7SL, were examined in HeLa and EBV-harboring cells. Because of possible functional similarities between EBERs and the adenovirus-associated (VA) RNAs, VAI was also localized; it appeared to be in the nucleus and cytoplasm, implying that VAI may have a different role than that of the nuclear-localized EBERs.

Cell Nucleus↗

PubMed1996

[Detection of a new small RNA, induced by heat shock, in wheat seed ribosomes].

Changes in the small cytoplasmic RNA (scRNA) composition have been examined in wheat embryos exposed to heat shock conditions. A novel scRNA of about 135 nucleotides in length termed as 5.3S RNA, has been detected for the first time. With a rise in temperature from 26 degrees C up to 37 degrees C, the amount of 5.3S RNA increases 5 to 6 times. It was found that 5.3S RNA is localized predominantly on ribosomes and also in the fraction of native 40S ribosomal subunits known to contain translation preinitiation complexes. Upon dissociation of 80S monoribosomes under high ionic strength conditions (0.5 M KCl), 5.3S RNA remains to be bound to the 40S subunit, thus indicating their strong and specific interaction. 5.3S RNA is neither a precursor of the 5S rRNA nor a discrete fragment of high molecular weight ribosomal RNA. It was supposed that 5.3S RNA is transcribed by RNA polymerase III and involved in protein synthesis regulation in plant cells under heat shock conditions at the level of translation initiation.

Base Sequence↗

PubMed1993

Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent.

The traditional morphologically grounded placement of South American guinea pig-like rodents (Caviomorpha) within one of the two rodent suborders, Hystricognathi, has been disputed by recent analysis of protein and nucleic acid sequence data. The Caviomorpha and possibly all Hystricognathi would be considered a separate order, distinct from the other rodent suborder, Sciurognathi, and thus of the order Rodentia, and would be placed closer phylogenetically to other mammals [Graur, D., Hide, W. A. & Li, W.-H. (1991) Nature (London) 351, 649-652]. To address the discrepancy between morphological comparisons and sequence analyses, we have applied an alternative form of molecular analysis. We demonstrate that BC1 RNA, a neural-specific small cytoplasmic RNA that is the product of a retropositionally generated gene (a gene derived by reverse transcription of RNA followed by insertion of the DNA copy into the genome), is present in Sciurognathi and guinea pig but not in other mammalian orders including Lagomorpha, Artiodactyla, and Primates. The species-confined, tissue-specific expression of a retroposed sequence therefore supports the morphological evidence for monophyly of Rodentia inclusive of guinea pig and demonstrates the usefulness of such molecular genetic markers. Furthermore, the conservation and tissue-specific expression of the BC1 RNA gene in the two divergent rodent suborders suggests that this macromolecule has been exapted into a functional role (i.e., coopted into a variant or novel function) in the rodent nervous system.

Animals↗

PubMed1997

Expression of dendritic BC200 RNA, component of a 11.4S ribonucleoprotein particle, is conserved in humans and simians.

Primate BC200 RNA, a brain-specific small cytoplasmic RNA, is one of the few known cell type specific non-messenger RNAs. It originated from a monomeric Alu short interspersed repetitive element (SINE) in primates. In situ hybridization using rhesus monkey (Macaca mulatta) brain sections reveals a similar cellular and sub-cellular distribution as in human brain. In addition to confirming its dendritic location, the distribution in an old world monkey indicates a discrete regional and subcellular location of BC200 RNA. We also report that BC200 RNA exists as a ribonucleoprotein (RNP) particle in vivo. In sucrose gradients, the BC200 particle has a sedimentation constant of about 11.4 S, significantly more than the corresponding 200 nucleotide long naked RNA (approximately 7.6 S).

Animals↗

PubMed1988

Low molecular weight RNA of Drosophila cells which is induced by heat shock--II. Structural properties.

Heat shock-induced small cytoplasmic RNA (HSI scRNA) from Drosophila culture cell was larger in size after dimethylchloroacetal treatment than in 7 M urea. Judging from its thermal denaturation profile and the nuclease S1 digestion experiment it was supposed that HSI scRNA is double-stranded. Nucleotide sequence analysis of the scRNA also suggested that it is double-stranded RNA with the blunt-ends.

Animals↗

PubMed2000

Endoribonuclease RNase III is essential in Bacillus subtilis.

The rncS gene of Bacillus subtilis encodes Bs-RNase III, a narrow-specificity endoribonuclease. Previous attempts to disrupt rncS were unsuccessful. Here, a strain was constructed in which Bs-RNase III expression was dependent upon transcription of rncS from a temperature-sensitive plasmid. Growth of this strain at the non-permissive temperature resulted in 90-95% cell death, and virtually all the cells that survived retained the rncS-expressing plasmid. Thus, we conclude that rncS is essential in B. subtilis. The rncS conditional strain also revealed that Bs-RNase III participates in the processing of ribosomal RNA, in addition to processing small cytoplasmic RNA, a member of the signal recognition particle RNA family. Most significantly, a rare rncS null strain was isolated that will aid further study of the critical role Bs-RNase III plays in B. subtilis.

Bacillus subtilis↗

PubMed1993

BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element.

We demonstrate that the BC200 RNA gene, which encodes a neural small cytoplasmic RNA, is a member of the most prodigious family of interspersed repetitive DNA and that its product represents an example of a primate tissue-specific RNA polymerase III transcript. The BC200 RNA gene is an early monomeric member and one of the few postulated transcriptionally active Alu sequences in this family of nearly half a million retropositionally amplified elements dispersed throughout the human genome. Furthermore, the isolation of two pseudogenes, BC200 beta and BC200 gamma, demonstrates the gene's transpositional ability. Interestingly, the BC200 beta pseudogene may have been generated by a conversion-like event after the human/chimpanzee divergence, resulting in an exchange of the left arm of a dimeric Alu element with the BC200 RNA coding sequence. Our data on conserved features of the active BC200 alpha gene suggest that its RNA product has been "exapted" into a function of the primate brain and provides a selective advantage to the species.

Animals↗

PubMedDate not supplied

[Small cytoplasmic poly(A)+RNA, homologous to the B2 repetitive sequence of the mouse genome, is present in ribonucleoproteins].

Small cytoplasmic poly(A) + RNA homologous to a highly repeated sequence B2 of the mouse genome (scB2 RNA) was not found as free RNA within a cell. This RNA is bound to small (12-18S) ribonucleoprotein particles as well as to heavy RNP particles, apparently informosomes. After deproteinization of the heavy RNP the major part of scB2 RNA molecules cosedimented with heavy RNAs. It seems that scB2 RNA is associated with mRNA in informosomes via short complementary regions. About half of the scB2 RNA molecules was revealed in the cytoskeleton fraction. The possibility that scB2 RNAs are involved in mRNA transport or in the regulation of mRNA translation is discussed.

Animals↗

PubMed1983

Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein.

A mouse monoclonal antibody and human autoimmune sera directed against various classes of small ribonucleoprotein particles have been tested for inhibition of mRNA splicing in a soluble in vitro system. The splicing of the first and second leader exons of adenovirus late RNA was inhibited only by those sera that reacted with U1 RNP. Both U1 RNP-specific human autoimmune serum and sera directed against the Sm class of small nuclear RNPs, including a mouse monoclonal antibody, specifically inhibited splicing. Antisera specific for U2 RNP had no effect on splicing nor did antisera specific for the La or Ro class of small RNPs. These results suggest that U1 RNP is essential for the splicing of mRNA precursors.

Adenoviruses, Human↗

PubMed1997

Prevalence of 13 autoantibodies and of the 16/6 and related pathogenic idiotypes in 465 patients with systemic lupus erythematosus and their relationship with disease activity.

With a cross sectional study of 465 consecutive systemic lupus erythematosus (SLE) patients tested for 13 autoantibodies (Aab) and two idiotypes we determined the prevalence of Aab according to disease activity, both general and at particular organ systems. Seventy seven percent of SLE sera had at least one Aab and 56% had it at high titres. Pathogenic idiotypes had a prevalence of less than 10% and 166 sera had Aab to 5 or more antigens and 9 sera had Aab against all 13 antigens tested. Patients with active disease had increased prevalence of Aab to DNP, ssDNA, ENA, mitochondria and histones when considered at 5 s.d. above the mean of normal controls. The higher positivity of Aab in patients with active disease was confirmed in logistic regression analysis adjusted by age, disease duration, and intensity of treatment. A trend was observed of increased prevalence and titres of Aab from inactive disease without treatment, to inactive disease but still being treated, to active disease. Only 22% of patients with active disease had no Aab and the higher the number of Aab the higher the frequency of active disease. Patients with active arthritis, and to a lesser degree those with active mucocutaneous involvement, had higher prevalence and titres of most autoantibodies than patients with disease activity at other organ systems. Active renal disease associated only with anti-dsDNA, whereas active CNS disease associated with anti-mitochondrial Aab. Our findings support the vision of SLE as an immune dysregulation leading to polyclonal B cell activation with resulting production of multiple Aab. Their profiles seem influenced by genetical, hormonal and environmental factors and, in turn, they contribute to the clinical picture in each patient. Disease activity influences the presence of some, but not all, Aab and some of them may remain present in some patients, even in remission.

Adult↗

PubMed1988

Identification of an essential Schizosaccharomyces pombe RNA homologous to the 7SL component of signal recognition particle.

We have cloned the gene encoding a novel small cytoplasmic RNA from the fission yeast Schizosaccharomyces pombe. Four lines of evidence support the idea that this RNA is a homolog of the 7SL RNA component of mammalian signal recognition particle (SRP), which targets presecretory proteins to the endoplasmic reticulum membrane. First, it shares limited but significant primary sequence homology with previously identified 7SL RNAs and can be folded into a similar secondary structure. Second, it possesses the 5' triphosphate characteristic of unprocessed RNA polymerase III transcripts, and moreover, it is the only fission yeast RNA in this size range with such a terminus. Third, its behavior in cell fractionation experiments suggests that it is part of a small ribonucleoprotein which forms salt-labile contacts with larger structures. Fourth, the particle containing S. pombe 7SL RNA resembles mammalian SRP in both size (11S) and affinity for DEAE-Sepharose. Disruption of the single-copy gene, designated slr1+, reveals that the RNA is indispensable for growth in fission yeast. This result is not surprising, since secretion is an essential cellular process.

Base Sequence↗

PubMed2002

Nucleolin associates with a subset of the human Ro ribonucleoprotein complexes.

Ro RNPs are evolutionarily conserved, small cytoplasmic RNA-protein complexes with an unknown function. In human cells, Ro RNPs consist of one of the four hY RNAs and two core proteins: Ro60 and La. Recently, the association of hnRNP I and hnRNP K with particles containing hY1 and hY3 RNAs has been described. The association of three other proteins, namely calreticulin, Ro52 and RoBPI, with (subsets of) the Ro RNPs is still controversial. To gain more insight into the composition and function of the Ro RNPs, we have immunopurified these particles from HeLa cell extracts using monoclonal antibodies against Ro60 and La. Using this approach, we have identified the RNA-binding protein nucleolin as a novel subunit of Ro RNP particles containing hY1 or hY3 RNA, but not hY4 and hY5 RNA. Using an in vitro hY RNA-binding assay we established that the internal pyrimidine-rich loop of hY1 and hY3 RNA is essential for the association of nucleolin. The binding is critically dependent on the presence of all four RNP motifs of nucleolin, but not of the C-terminal RGG-box. Moreover, we demonstrate that, in contrast to nucleolin and hnRNP K, nucleolin and hnRNP I can bind simultaneously to the internal pyrimidine-rich loop of hY1 RNA. We postulate that nucleolin functions in the biogenesis and/or trafficking of hY1 and hY3 RNPs through the nucleolus and subsequent transport to the cytoplasm.

Autoantigens↗

PubMed1982

The sequences homologous to major interspersed repeats B1 and B2 of mouse genome are present in mRNA and small cytoplasmic poly(A) + RNA.

Heavy nuclear RNA contains high amounts of transcripts from repetitive sequences B1 and B2. Cytoplasmic poly(A)+RNA and, particularly, polysomal poly(A)+RNA (mRNA) also include these sequences but in smaller amounts. The abundant 2 kb mRNA of mouse liver are found to have a B2 sequence. These sequences are also found in a new class of low-molecular-weight heterogeneous (200-400 nucleotide long) poly(A)+RNAs. These RNAs are located mostly in cytoplasm rather than in polysomes. The amount of small B2+ RNAs is noticeable larger than that of small B1+ RNAs. Tumour cells seem to contain more small B2 RNA than normal cells. The hybridization tests show that extended homology exists between the B1 sequence and 4.5S small nuclear RNA, which is predicted from comparison of their base sequences. Also, we have found homology between B1 and small cytoplasmic 7S RNA. Hybridization of B2 to sn or sc RNAs has not been observed, although the sequencing reveals partial homology between B2 and 4.5S sn RNAI /1/.

Animals↗

PubMed1992

The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19.

Translocation of proteins across the endoplasmic reticulum (ER) membrane represents the first step in the eukaryotic secretory pathway. In mammalian cells, the targeting of secretory and membrane protein precursors to the ER is mediated by signal recognition particle (SRP), a cytosolic ribonucleoprotein complex comprising a molecule of 7SL RNA and six polypeptide subunits (relative molecular masses 9, 14, 19, 54, 68 and 72K). In Saccharomyces cerevisiae, a homologue of the 54K subunit (SRP54) co-purifies with a small cytoplasmic RNA, scR1 (refs 4, 5). Genetic data indicate that SRP54 and scR1 are involved in translocation in vivo, suggesting the existence of an SRP-like activity in yeast. Whether this activity requires additional components similar to those found in mammalian SRP is not known. We have recently reported a genetic selection that led to the isolation of a yeast mutant, sec65-1, which is conditionally defective in the insertion of integral membrane proteins into the ER. Here we report the cloning and sequencing of the SEC65 gene, which encodes a 31.2K protein with significant sequence similarity to the 19K subunit of human SRP (SRP19). We also report the cloning of a multicopy suppressor of sec65-1, and its identification as the previously defined SRP54 gene, providing genetic evidence for an interaction between these gene products in vivo.

Amino Acid Sequence↗

PubMedDate not supplied

[Enhanced transcription of genes of the intracisternal A particles and B2 elements in mouse tumors].

A comparison of the expression of two mobile genetic elements A1 and B2 was studied in normal and tumor tissues. The A1 element is a chromosomal homolog of IAP genes, and B2 is a short ubiquitous repetitive sequences of the mouse genome. These sequences were earlier cloned in our laboratory and in this study were used as probes in hybridization experiments with RNA isolated from different mouse tumor and normal tissues. Both elements were efficiently transcribed in tumor cells. The level of expression of A1 sequences in tumors was 100-200 times higher than in normal tissues. The amount of B2 small cytoplasmic RNA significantly varied in different normal tissues. The content of this RNA was much higher in tumors. Closed circular DNA molecules containing IAP sequences were found in Ehrlich carcinoma cells. These DNA molecules are considered as intermediate forms of the mobile elements. The role of these mobile elements in the regulation of RNA expression and tumor progression is discussed.

Animals↗

PubMed1994

A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors.

The Ro autoantigen is a 60-kD protein that is usually found in small cytoplasmic RNA-protein complexes known as Ro RNPs. Although the Ro RNPs are abundant and conserved components of a variety of vertebrate and invertebrate cells, their function is unknown. We have discovered that the Ro protein is also found complexed with certain variant 5S rRNAs in Xenopus oocytes. These RNAs contain one or more point mutations compared with the major oocyte 5S rRNA sequence as well as additional nucleotides at the 3' end. We demonstrate that the Ro protein binds specifically mutant 5S rRNAs containing 3' terminal extensions. These mutant RNAs are processed inefficiently to mature 5S rRNA and most eventually are degraded. The observation that the Ro autoantigen specifically associates with defective 5S rRNA precursors suggests that this protein may function as part of a novel quality control or discard pathway for 5S rRNA production.

Animals↗

PubMed1996

Sicca syndrome associated with hepatitis C virus infection.

OBJECTIVE: To determine the prevalence of hepatitis C virus (HCV) infection in patients with sicca syndrome, and to determine the clinical, immunologic, and genetic characteristics of sicca syndrome associated with HCV. METHODS: We conducted a prospective study in a university hospital immunology-rheumatology department. Sixty-two consecutive patients with sicca syndrome according to the European criteria for Sjögren's syndrome were included. HCV infection was diagnosed in patients with positive recombinant immunoblot assay findings and the presence of viral RNA in serum and saliva. Rheumatoid factor (RF), cryoglobulins, antinuclear antibodies, and anti-SS-A/SS-B antibodies were sought. HLA typing was performed on all patients. RESULTS: The prevalence of HCV infection in patients with sicca syndrome was 19%. The incidence of neurologic involvement was significantly increased in patients with sicca syndrome associated with HCV infection (24% versus 4%; P < 0.03), as was elevations in transaminase levels (87.5% versus 16%; P < 0.0001). RF and cryoglobulins were more frequent in HCV-positive sicca syndrome patients (62% versus 30%; P < 0.03, and 56% versus 10%; P < 0.001, respectively). In contrast, anti-SS-A/SS-B antibodies were present in 38% of HCV-negative sicca syndrome patients, but in only 1 HCV-positive sicca syndrome patient (P < 0.01). No significant difference in HLA type was observed. Viral RNA was present in the saliva of 83% of HCV-positive sicca syndrome patients, but in none of the HCV-negative sicca syndrome patients. CONCLUSION: We observed a high prevalence of HCV infection in our patients with sicca syndrome. HCV-positive sicca syndrome patients had specific clinical characteristics and were seronegative for SS-A/SS-B antibodies. Moreover, HCV RNA was present in the saliva of patients with HCV-associated sicca syndrome.

Antibodies↗

PubMed1994

Identification and characterization of host factor interactions with cis-acting elements of rubella virus RNA.

We have analyzed the function of cis-acting elements of rubella virus RNA and the components which interact with these elements in viral RNA replication. We demonstrated that the 5'- and 3'-terminal sequences from RV RNA promote translation and negative-strand RNA synthesis of chimeric chloroamphenicol acetyltransferase (CAT) RNAs. These sequences have a potential to form stem-loop (SL) structures and bind cellular proteins specifically in RNA gel-shift and UV cross-linking assays. The 5' end binding proteins were identified to be Ro/SSA-associated antigens by virtue of being recognized in an RNA complex by an autoimmune patient serum with Ro antigen type specificity. Purification and sequence analysis of the 3' end binding protein revealed that it is a homologue of human calreticulin. The role of host protein in RV replication is discussed.

Autoantigens↗