SEARCH · PubMed Health

Results for “noncoding RNA”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,585 records · Page 88Linked to original sources

PubMed2002

Interaction of translation initiation factor eIF4B with the poliovirus internal ribosome entry site.

Poliovirus translation is initiated at the internal ribosome entry site (IRES). Most likely involving the action of standard initiation factors, this highly structured cis element in the 5" noncoding region of the viral RNA guides the ribosome to an internal silent AUG. The actual start codon for viral protein synthesis further downstream is then reached by ribosomal scanning. In this study we show that two of the secondary structure elements of the poliovirus IRES, domain V and, to a minor extent, domain VI, are the determinants for binding of the eukaryotic initiation factor eIF4B. Several mutations in domain V which are known to greatly affect poliovirus growth also seriously impair the binding of eIF4B. The interaction of eIF4B with the IRES is not dependent on the presence of the polypyrimidine tract-binding protein, which also binds to the poliovirus IRES. In contrast to its weak interaction with cellular mRNAs, eIF4B remains tightly associated with the poliovirus IRES during the formation of complete 80S ribosomes. Binding of eIF4B to the IRES is energy dependent, and binding of the small ribosomal subunit to the IRES requires the previous energy-dependent association of initiation factors with the IRES. These results indicate that the interaction of eIF4B with the 3" region of the poliovirus IRES may be directly involved in translation initiation.

5' Untranslated Regions↗

PubMed1987

Cell cycle regulation of a mouse histone H4 gene requires the H4 promoter.

The mouse histone H4 gene, when stably transformed into L cells on the PSV2gpt shuttle vector, is cell cycle regulated in parallel with the endogenous H4 genes. This was determined in exponentially growing pools of transformants fractionated into cell cycle-specific stages by centrifugal elutriation, a method for purifying cells at each stage of the cell cycle without the use of treatments that arrest growth. Linker additions in the 5' noncoding region of the H4 RNA or in the coding region of the gene did not affect the cell cycle-regulated expression of the modified H4 gene even though the overall level of expression was altered. However, replacing the H4 promoter with the human alpha-2 globin promoter, so that the histone transcript produced by the chimeric gene remains essentially unchanged, resulted in the constitutive expression of H4 mRNA during all phases of the cell cycle with no net increase in H4 mRNA levels during the G1-to-S transition. From these results we conclude that all the information necessary for the cell cycle-regulated expression of the H4 gene is contained in the 5.2-kilobase subclone used in these studies with 228 nucleotides of 5'-flanking DNA and that the increase in H4 mRNA during the G1-to-S transition in the cell cycle is mediated by the H4 promoter and not by the increased stability of the H4 RNA.

Animals↗

PubMed1992

[Recent advances in laboratory tests for liver diseases].

Many tests for hepatitis C virus (HCV) infection have been developed and have proved useful for prevention of post-blood transfusion hepatitis C. However, there are at least 4 genotypes of HCV and the predominant type is different among countries. None of the tests using antigens from one genotype are sensitive in detecting the antibodies against another genotype. More sensitive tests using a more stable part of the HCV RNA sequences such as 5'-noncoding region must be developed for clinical use. Automated PCR methods and DNA sandwich hybridization methods using branched DNA amplification multimers may be candidates. Recently a hepatocyte growth factor test has been developed in Japan. Multicenter trials of this test reveal that it is useful for assessment of acute severe hepatitis. Tests for collagen type IV, fibronectin receptor, and prolyl hydroxylase have been reported useful for assessment of liver fibrosis. However, serum prolyl hydroxylase is prone to increase in response to hepatocellular damage as well as fibrotic processes. Enzymatic methods for determination of branched amino acids and tyrosine have been developed. The molar ratio of branched amino acids to tyrosine seems to have same pathophysiological meaning as the ratio of branched amino acids to aromatic amino acids (Fischer ratio) in assessment of liver cirrhosis. Lidocaine test is reported to be useful for predicting survival of transplanted liver and also assessing the function of the cirrhotic liver. Profiles of alpha-fetoprotein subfractions based on lectin-reactivity and galactosyl transferase II isoenzyme have been reported to be useful for detecting hepatocellular carcinoma but this remains to be proved.

Clinical Laboratory Techniques↗

PubMed1992

Linker scanning mutagenesis of the internal ribosome entry site of poliovirus RNA.

The initiation of cap-independent translation of poliovirus mRNA occurs as a result of ribosome entry at an internal site(s) within the 5' noncoding region. A series of linker scanning mutations was constructed to define the genetic determinants of RNA-protein interactions that lead to high-fidelity translation of this unusual viral mRNA. The mutations are located within two distinct stem-loop structures in the 5' noncoding region of poliovirus RNA that constitute a major portion of a putative internal ribosome entry site. On the basis of our data derived from genetic and biochemical assays, the stability of one of the stem-loop structures appears to be essential for translation initiation via internal binding of ribosomes. However, the second stem-loop structure may function in a manner that requires base pairing and proper spacing between specific nucleotide sequences. By employing RNA electrophoretic mobility shift assays, an RNA-protein interaction was detected for this latter stem-loop structure that does not occur in RNAs containing mutations which perturb the predicted hairpin structure. Analysis of in vivo-selected virus revertants, in combination with mobility shift assays, suggests that extensive genetic rearrangement can lead to restoration of 5' noncoding region functions, possibly by the repositioning of specific RNA sequence or structure motifs.

Base Sequence↗

PubMed1995

Specificity in the association of tomato black ring virus satellite RNA with helper virus.

The satellite RNAs (sat-RNAs) associated with some isolates of tomato black ring virus (TBRV) consist of single-stranded molecules of about 1375 nucleotides, encoding a nonstructural protein of 48K which has been shown to be involved in the replication of the sat-RNA. The TBRV sat-RNAs are also dependent for their replication and for their encapsidation on the helper virus. To characterize the nature of the association between sat-RNA and helper virus, transcripts of sat-RNA from TBRV isolates C and L (respectively, of serotypes G and S) have been prepared and inoculated onto Chenopodium quinoa leaves or protoplasts. Transcript of the TBRV sat-RNA C is efficiently multiplied when coinoculated with the genomic RNAs of TBRV isolate G (used instead of TBRV isolate C, because isolate G was depleted of sat-RNA), but does not multiply with TBRV isolate L. On the other hand, transcript of the sat-RNA L is able to multiply with the cognate helper virus and, less efficiently, with grapevine chrome mosaic virus (another nepovirus, 80% similar to TBRV), but does not multiply with TBRV G. The specificity of the association resides at the level of sat-RNA replication. Analysis of the multiplication of chimeric sat-RNAs, obtained by exchanging different regions between the two sat-RNAs C and L, showed that the 5' and the 3' noncoding regions of the sat-RNA, although important for replication, are not implicated in specificity. The results suggest that the determinants of the specificity are contained in the 48K sat-RNA-encoded protein.

Base Sequence↗

PubMed1992

Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: relationship to genotypes of hepatitis C virus.

To investigate the relationship between genotypes of hepatitis C virus and response to interferon-alpha therapy, hepatitis C virus RNA was assayed by polymerase chain reaction with three sets of primers and probes in 70 patients with non-A, non-B chronic hepatitis who received interferon-alpha. Twenty-four patients sustained long-term remissions (complete responders). Polymerase chain reaction for 5'-terminal noncoding region detected hepatitis C virus RNA in 94.3% (66 of 70) of the patients. Polymerase chain reaction for nonstructural region 3, in which primers and a probe were synthesized to be identical to hepatitis C virus-J, detected hepatitis C virus RNA in 40 patients. Polymerase chain reaction for nonstructural region 5-in which sequences of primers and a probe were derived from hepatitis C virus-K2, a genotype different from hepatitis C virus-J--detected hepatitis C virus RNA in 17 patients. Only one patient was positive on both nonstructural region 3 and nonstructural region 5 polymerase chain reaction. Nucleotide sequence of clones obtained from 5' terminal noncoding region polymerase chain reaction products of two patients positive on polymerase chain reaction for nonstructural region 3 and negative on polymerase chain reaction for nonstructural region 5 (group 1) corresponded to that of the hepatitis C virus-J group, and those of clones from two patients negative on polymerase chain reaction for nonstructural region 3 and positive on polymerase chain reaction for nonstructural region 5 (group 2) corresponded to that of hepatitis C virus-K2.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1998

Recombinant dengue virus type 1 NS3 protein exhibits specific viral RNA binding and NTPase activity regulated by the NS5 protein.

The full-length dengue virus NS3 protein has been successfully expressed as a 94-kDa GST fusion protein in Escherichia coli. Treatment of the purified fusion protein with thrombin released a 68-kDa protein which is the expected molecular mass for the DEN1 NS3 protein. The identity of this protein was confirmed by Western blotting using dengue virus antisera. Two related activities of the recombinant NS3 protein were characterized, which were the binding of the protein to the 3'-noncoding region of the dengue virus RNA genome and NTPase activity. We demonstrated using a band shift assay that the DEN1 NS3 protein could form a complex with the stem-loop structure in the 3'-noncoding region (3'-NCR), although sites outside the stem-loop may also participate in binding. Using various unlabeled homopolymeric and heteropolymeric RNAs as competitors for binding, it was further shown that the DEN1 NS3 protein exhibits preferential binding to a 94-nt RNA transcript from the 3'-NCR of the dengue virus. The NTPase activity of the recombinant DEN1 NS3 protein was characterized using a thin-layer chromatography assay. We found that the DEN1 NS3 protein possesses some aspects of NTPase activity, which are distinct from those found in other flaviviruses. Although the NS3 protein was able to utilize all four ribonucleoside triphosphates as its substrates, the NS3 protein showed a distinct preference for purine triphosphates (i.e., ATP and GTP). The addition of poly(U) did not stimulate NTPase activity in DEN1 NS3 protein, which contrasts with the reports for other flaviviral NS3 proteins. However, NTPase activity was specifically stimulated by the viral NS5 protein, which was manifested by a more than twofold increase in the rate of ATP hydrolysis and a 25% increase in the yield of ADP at the end of a 120-min reaction. These data suggest that the NTPase activity of the NS3 protein may be regulated by the viral NS5 protein during virus replication.

Adenosine Triphosphatases↗

PubMed1996

Comparison of two quantitative hepatitis C virus reverse transcriptase PCR assays.

A quantitative hepatitis C virus reverse transcriptase PCR (HCV RT-PCR) assay established in our laboratory was compared with the Roche Amplicor HCV Monitor test kit for agreement of test results and intra-assay variability. Both assays rely on reverse transcription and amplification of extracted RNA from patients' sera together with an internal RNA standard derived from the 5'-noncoding region of HCV. A panel of clinical serum samples (n = 33) was quantitatively analyzed in parallel by both test systems. The methods demonstrated substantial agreement between 1 x 10(3) and 5 x 10(5) HCV RNA molecules per ml of serum. However, with sera containing more than 5 x 10(5) copies per ml, according to our in-house assay, the results diverged on average in a nonacceptable range of 2 orders of magnitude. Our in-house HCV RT-PCR assay measured up to 5 x 10(7) HCV-RNA molecules per ml in some serum samples. However, the Roche Amplicor HCV Monitor test kit did not detect more than 2 x 10(6) molecules in any of the serum samples tested. After dilution of serum samples prior to testing, an approximately 0.5 order of magnitude more HCV RNA molecules was detected by the Roche HCV test kit in sera containing high copy numbers (> 5 x 10(5) RNA copies according to the in-house assay). The in-house PCR and the Roche Amplicor HCV Monitor test kit revealed coefficients of variation of 6.2 and 7.5%, respectively.

Base Sequence↗

PubMed1997

Response to interferon of GB virus C and hepatitis C virus in patients with chronic hepatitis.

OBJECTIVES: To evaluate the response to interferon and capacity to induce liver disease of a putative non-A to E hepatitis virus designated GB virus C (GBV-C). METHODS: RNA of GBV-C was detected by reverse transcription polymerase chain reaction with nested primers deduced from the 5'-noncoding region. It was titrated, along with RNA of hepatitis C virus (HCV), in 16 co-infected patients (11%) out of 140 patients who received interferon. RESULTS: At the completion of a 6-month course of interferon (total dose: 516-774 million units), GBV-C RNA disappeared from serum in seven (44%) and HCV RNA from serum in 11 (69%) patients. At 6 months after interferon treatment ended, GBV-C RNA remained cleared in three patients (19%), and HCV RNA was persistently undetectable in four (25%). One patient lost both GBV-C and HCV RNAs. The three patients whose serum was cleared of GBV-C RNA had pretreatment titers of the virus (two with 10[1]/ml and one with 10[2]/ml) that were considerably lower than the titers of 13 patients (one with 10[2]/ml, eight with 10[3]/ml, and four with > or = 10[4]/ml) without such clearance. The decrease in alanine aminotransferase levels paralleled the response of HCV RNA but not that of GBV-C RNA to interferon. The response of HCV at 6 months after interferon in the co-infected patients (4/16 or 25%) did not differ significantly from that in patients without GBV-C infection (44/124 or 35%). CONCLUSIONS: The sensitivity of GBV-C to interferon is comparable to but independent of HCV. Co-infection with GBV-C does not influence the response to interferon of patients with chronic hepatitis C.

Antiviral Agents↗

PubMed1994

[Diagnosis of type C chronic hepatitis using PCR technology].

Many studies have suggested that examination of a patient's serum for viral RNA by reverse transcriptase-polymerase chain reaction (RT-PCR) is the most sensitive and specific serological means of determining chronic HCV infection. Moreover, technique to quantify HCV RNA in serum using PCR technology has been developed, and diagnosis of HCV genotype by PCR with mixed primers has been used for diagnosis of type C hepatitis. Herein, we discuss the laboratory technique and significance of various PCR methods. HCV RNA can be detected by amplification technique of RT-PCR. Primers in the 5'-noncoding region are frequently used to detect HCV RNA, because the RNA sequence in this region is the most conserved. We usually perform 30 cycles of amplification with outer primers and another 30 cycles with inner primers (nested RT-PCR). Using this technique, HCV RNA was detected in 96% of anti-HCV-positive chronic hepatitis patients. This PCR technique gives us important information for the diagnosis of type C chronic hepatitis indicating HCV infection. The competitive PCR technique is usually used to quantify HCV RNA. This method is based on complification of the target RNA with known amounts of synthetic mutant RNA. The mutant RNA should be amplified by the same primers for amplifying target RNA, and should be distinguished from target RNA by the size of the amplified DNA product by making a deletion or restriction site artificially. Quantifying HCV RNA before interferon therapy is useful to predict the effectiveness of the therapy; patients with a large amount of HCV RNA tend to have a poor outcome.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1979

Characterization of messenger RNA for fructose 1,6-bisphosphate aldolase A isozyme of rat ascites hepatoma AH 7974 cells.

The messenger activity for fructose 1,6-bisphosphate aldolase (EC4.1.2.13) (aldolase) A isozyme has been characterized in the polysome- or the messenger RNA-directed, protein-synthesizing system using the pH 5 fraction of rat liver or wheat germ extracts, respectively. The subunit of aldolase A synthesized in vitro was detected by immunoprecipitation with anti-aldolase A antibody raised in chickens followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The synthesis of the enzyme depended on the addition of polysomes or polyadenylate-containing RNA of rat ascites hepatoma AH 7974 cells which show a complete shift of aldolase isozyme to type A, whereas polysomes of adult rat liver were inactive. The messenger activity for aldolase A was present exclusively on free polysomes but absent on membrane-bound polysomes and in the soluble supernatant fraction of AH 7974 cells. The size of aldolase A messenger RNA determined by formamide-containing sucrose density gradient centrifugation was approximately 5.8 X 10(5) daltons corresponding to 1650 nucleotides. Taking into account the number of amino acid residues in the aldolase A subunit, approximately 400 nucleotides correspond to the noncoding region of aldolase A messenger RNA.

Animals↗

PubMed1994

Epidemiological studies on hepatitis C virus infection: detection, prevalence, exposure and prevention.

Highly sensitive and specific tests for HCV infection are now available for epidemiological studies. These include: (1) the second-generation ELISA or agglutination technique with supplemental testing; (2) serotyping of antibody; (3) detection of HCV-RNA by RT-nested double PCR with the 5' noncoding region for the highest sensitivity; (4) quantitation of HCV-RNA; (5) genotyping using specific primers in the core region, and (6) sequence analysis of E2/NS1 hypervariable region 1 to identify homology among HCV isolates. Transmission of HCV is commonly done by percutaneous routes, although the route in a significant proportion of sporadic infections is unknown. Sexual transmission and perinatal transmission appear to be relatively infrequent.

Africa↗

PubMed2006

Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction.

Recent studies have uncovered extensive presence and functions of small noncoding RNAs in gene regulation in eukaryotes. In particular, RNA interference (RNAi) has been the subject of significant investigations for its unique role in post-transcriptional gene regulation and utility as a tool for artificial gene knockdown. Here, we describe a novel strategy for post-transcriptional gene regulation in mammalian cells in which RNAi is specifically modulated through RNA aptamer-small molecule interaction. Incorporation of an RNA aptamer for theophylline in the loop region of a short hairpin RNA (shRNA) designed to silence fluorescent reporter genes led to dose-dependent inhibition of RNAi by theophylline. shRNA cleavage experiments using recombinant Dicer demonstrated that theophylline inhibited cleavage of an aptamer-fused shRNA by Dicer in vitro. Inhibition of siRNA production by theophylline was also observed in vivo. The results presented here provide the first evidence of specific RNA-small molecule interaction affecting RNAi, and a novel strategy to regulate mammalian gene expression by small molecules without engineered proteins.

Aptamers, Nucleotide↗

PubMed1999

Is hepatitis G/GB virus-C virus hepatotropic? Detection of hepatitis G/GB virus-C viral RNA in liver and serum.

The recently identified hepatitis G virus (HGV, also named GB virus-C, GBV-C) appears to have similarities to hepatitis C virus and other flaviviridae. To better understand its clinical significance and hepatotropism, we collected liver tissue and matched serum samples from 56 patients undergoing liver transplantation. HGV/GBV-C RNA was detected by reverse transcription-nested PCR, using primers from the relatively conserved 5' noncoding region of the genome to detect HGV/GBV-C RNA and the amount was semiquantitatively estimated by serial 10-fold endpoint dilution. The presence and amount of HCV RNA was estimated by the same methodology. Seventeen patients (30%) had HGV/GBV-C RNA detectable either in liver or in serum, including two of three with cryptogenic liver disease. Interestingly, 5 of 17 (29%) patients had HGV/GBV-C RNA in serum but not liver, even with repeated testing of hepatic RNA from different portions of the liver. Furthermore, the titer of HGV/GBV-C RNA was significantly lower in liver than in serum in most samples (mean log titer, 1.33 vs. 2.56, P < 0.05). In contrast, all 21 patients with HCV RNA in serum also had the virus detectable in liver. In five patients coinfected with HCV and HGV/GBV-C, the mean titer of HCV RNA in liver was higher than that in serum (log titer, 2.8 vs. 3.0, P > 0.05). Thus, our results suggest that HGV/GBV-C is probably not hepatotropic and may replicate predominantly in sites other than the liver. These findings brings into question the role of HGV in causing significant liver disease.

5' Untranslated Regions↗

PubMed1999

Temporal and spatial analysis of Sin Nombre virus quasispecies in naturally infected rodents.

Sin Nombre virus (SNV) is thought to establish a persistent infection in its natural reservoir, the deer mouse (Peromyscus maniculatus), despite a strong host immune response. SNV-specific neutralizing antibodies were routinely detected in deer mice which maintained virus RNA in the blood and lungs. To determine whether viral diversity played a role in SNV persistence and immune escape in deer mice, we measured the prevalence of virus quasispecies in infected rodents over time in a natural setting. Mark-recapture studies provided serial blood samples from naturally infected deer mice, which were sequentially analyzed for SNV diversity. Viral RNA was detected over a period of months in these rodents in the presence of circulating antibodies specific for SNV. Nucleotide and amino acid substitutions were observed in viral clones from all time points analyzed, including changes in the immunodominant domain of glycoprotein 1 and the 3' small segment noncoding region of the genome. Viral RNA was also detected in seven different organs of sacrificed deer mice. Analysis of organ-specific viral clones revealed major disparities in the level of viral diversity between organs, specifically between the spleen (high diversity) and the lung and liver (low diversity). These results demonstrate the ability of SNV to mutate and generate quasispecies in vivo, which may have implications for viral persistence and possible escape from the host immune system.

Amino Acid Sequence↗

PubMed2024

Detection of mitochondrial tDRs in killifish embryos and other non-model organisms.

In recent years a diversity of small noncoding RNAs have been identified that originate from the mitochondrial genome. These mitosRNAs are often dominated by tRNA-derived small RNAs (mito-tDRs). Differential expression of mito-tDRs is associated with responses to stress. They also appear to be expressed differentially during development and their expression may be enriched in stress-tolerant animals. Very little is currently known about roles or modes of action of these sequences, although they are implicated in a diversity of processes such as cell cycle regulation, mRNA stability, regulation of ROS production, and import of proteins into the mitochondrion. To better understand the various roles these sequences may play, it is critical that we understand their diversity, cellular location, and the context for their expression. This protocol outlines the methodologies used to detect mitosRNAs, including mito-tDRs, in embryos and cells of the annual killifish Austrofundulus limnaeus. We highlight critical steps in the isolation of RNA, creation of sequencing libraries, bioinformatics processing of sequence data, and methods for validation of expression that support a robust discovery pipeline for mitosRNAs even from species with incomplete reference genome sequences.

Animals↗

PubMed2024

Small noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells.

BACKGROUND: Molecular techniques can complement conventional spermiogram analyses to provide new information on the fertilizing potential of spermatozoa and to identify early alterations due to environmental pollution. METHODS: Here, we present a multilevel molecular profiling by small RNA sequencing and sperm nuclear basic protein analysis of male germ cells from 33 healthy young subjects residing in low and high-polluted areas. RESULTS: Although sperm motility and sperm concentration were comparable between samples from the two sites, those from the high-pollution area had a higher concentration of immature/immune cells, a lower protamine/histone ratio, a reduced ability of sperm nuclear basic proteins to protect DNA from oxidative damage, and an altered copper/zinc ratio in sperm. Sperm levels of 32 microRNAs involved in intraflagellar transport, oxidative stress response, and spermatogenesis were different between the two areas. In parallel, a decrease of Piwi-interacting RNA levels was observed in samples from the high-polluted area. CONCLUSIONS: This comprehensive analysis provides new insights into pollution-driven epigenetic alterations in sperm not detectable by spermiogram.

Male↗

PubMed2003

A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA.

The 5' untranslated leader region of retroviral RNAs contains noncoding information that is essential for viral replication, including signals for transcriptional transactivation, splicing, primer binding for reverse transcription, dimerization of the genomic RNA, and encapsidation of the viral RNA into virions. These RNA motifs have considerable structural and functional overlap. In this study, we investigate the conformational dynamics associated with the use and silencing of a sequence in HIV-2 RNA that is involved in genomic RNA dimerization called stem-loop 1 (SL1) and its relationship with a flanking sequence that is known to be important for encapsidation of viral RNAs. We demonstrate that a long-distance intramolecular interaction between nucleotides located upstream of the primer-binding site domain and nucleotides encompassing the Gag translation start codon functionally silences SL1 as a dimerization element. This silencing can be relieved by mutation or by hybridization of an oligonucleotide that disrupts the long-distance interaction. Furthermore, we identify a palindrome within the packaging/encapsidation signal Psi (just 5' of SL1) that can either serve as an efficient dimerization signal itself, or can mediate SL1 silencing through base pairing with SL1. These results provide a tangible link between the functions of genomic RNA dimerization and encapsidation, which are known to be related, but whose physical relationship has been unclear. A model is proposed that accounts for observations of dimerization, packaging, and translation of viral RNAs during different phases of the viral replication cycle.

Base Sequence↗