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Results for “noncoding RNA”

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PubMed1995

Serial assay of hepatitis C virus RNA in serum for predicting response to interferon-alpha therapy.

To determine whether the loss of serum hepatitis C virus RNA (HCV-RNA) early in interferon therapy would indicate a sustained response to this agent, we detected serum HCV-RNA successively during and after therapy. Serum samples for detection of HCV-RNA were obtained serially from 36 patients with chronic hepatitis C treated with interferon-alpha. In 28 of these patients, results of the assay were compared with genotypes and quantitative levels of HCV-RNA in serum before therapy. HCV-RNA was detected by a reverse transcription polymerase chain reaction using the 5'-noncoding region as a primer. Genotypes were determined by using type-specific primers, and serum levels of HCV-RNA were determined by a competitive reverse transcription polymerase chain reaction (RT-PCR). HCV-RNA disappeared from serum in eight of 10 responders (80%), but in only one of the 26 nonresponders (3.8%) at the second week of therapy (P < 0.0005). The time until the disappearance of HCV-RNA was correlated with the serum level of HCV-RNA present before therapy (P < 0.05). The early disappearance of HCV-RNA from serum during interferon therapy was useful in predicting a sustained response in patients with chronic hepatitis C.

Adult↗

PubMed1992

Non-A, non-B chronic hepatitis is chronic hepatitis C: a sensitive assay for detection of hepatitis C virus RNA in the liver.

To study the role of hepatitis C virus in non-A, non-B chronic hepatitis, 49 liver biopsy samples from 40 patients with non-A, non-B chronic hepatitis and 9 control patients were analyzed by complementary DNA/polymerase chain reaction. Two segments of the HCV genome, one in the nonstructural region and the other in the noncoding region, were amplified by two sets of primer pairs. With use of the nonstructural region primers, hepatitis C virus RNA was detected in 24 (60%) of 40 patients with non-A, non-B chronic hepatitis. Of these 40 patients, RNA was detected in 19 (70%) of 27 patients positive for antibody to hepatitis C virus and in 5 (38%) of 13 patients negative for antibody to hepatitis C virus. However, with the noncoding region primers, hepatitis C virus RNA was detected in 38 (95%) of 40 patients with non-A, non-B chronic hepatitis. Of these patients, the RNA was detected in 26 (96%) of 27 patients positive for antibody to hepatitis C virus and also in 12 (92%) of 13 patients positive for antibody to hepatitis C virus. Hepatitis C virus RNA was not detected in any of the control patients. Sequence analysis showed homology between our samples and the prototype to be only 66% to 77% in the nonstructural region but 99% to 100% in the noncoding region. We conclude that almost all patients with non-A, non-B chronic hepatitis in Japan are currently infected with hepatitis C virus, regardless of the presence or absence of antibody to hepatitis C virus.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed2006

Spatial organization of transcription by RNA polymerase III.

RNA polymerase III (pol III) transcribes many essential, small, noncoding RNAs, including the 5S rRNAs and tRNAs. While most pol III-transcribed genes are found scattered throughout the linear chromosome maps or in multiple linear clusters, there is increasing evidence that many of these genes prefer to be spatially clustered, often at or near the nucleolus. This association could create an environment that fosters the coregulation of transcription by pol III with transcription of the large ribosomal RNA repeats by RNA polymerase I (pol I) within the nucleolus. Given the high number of pol III-transcribed genes in all eukaryotic genomes, the spatial organization of these genes is likely to affect a large portion of the other genes in a genome. In this Survey and Summary we analyze the reports regarding the spatial organization of pol III genes and address the potential influence of this organization on transcriptional regulation.

Animals↗

PubMed2003

Transcriptional silencing of an amoebapore gene in Entamoeba histolytica: molecular analysis and effect on pathogenicity.

Transcriptional silencing of the gene coding for amoebapore A (AP-A) was observed when trophozoites of Entamoeba histolytica were transfected with a hybrid plasmid construct containing the ap-a gene flanked by the upstream and downstream segments of the original Ehap-a gene. Transfectants were totally devoid of ap-a transcript and AP-A protein. An identical silencing effect was observed upon transfection with a plasmid that contained only the 5' upstream region of ap-a. Removal of the selecting antibiotic enabled the isolation of plasmidless clones, which retained in their progeny the silenced phenotype. E. histolytica cells were able to overexpress ap-a when transfected with a plasmid containing the gene flanked by the 5' and 3' regions of the EhRP-L21 gene. This plasmid, however, could not express ap-a in the retransfected, cloned trophozoites lacking AP-A. This is the first report of gene silencing in E. histolytica, and the mechanism appears to belong to transcriptional gene silencing and not to posttranscriptional gene silencing. This conclusion is based on the following results: (i) silencing was achieved by transfection of homologous 5' flanking sequences (470 bp of the Ehap-a gene), (ii) transcription initiation of Ehap-a was found to be blocked, and (iii) short double-stranded RNA fragments of the ap-a coding and noncoding sequences were not detected. Trophozoites lacking AP-A are nonpathogenic and impaired in their bacteriolytic capability.

3' Flanking Region↗

PubMed2006

Nonisotopic detection of microRNA using digoxigenin labeled RNA probes.

MicroRNAs (miRNAs) are an important class of endogenously derived, small approximately 22 nucleotide noncoding regulatory RNAs that have recently become implicated in development, cell regulation and cancers of various tissues. Here we report a nonisotopic Northern analysis method for miRNA detection using 3'-digoxigenin (DIG)-labeled RNA oligo probes. Northern blot analysis was performed using miRNA or total RNA fractions extracted from human leukemic cell lines, and blots were hybridized with either 32P- or DIG-labeled RNA probe for miR-181, miR-155 or miR-16. A labeled probe for U6 small nuclear RNA served as an internal control. The use of DIG-labeled RNA probes was equally sensitive compared to 32P-labeled probes in detecting miRNA quantities as low as 50 ng. The ability to use nonisotopic methods and yet obtain sensitive and reliable results offers an advantage to investigators who prefer to avoid isotopes.

Blotting, Northern↗

PubMed2000

Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco.

Posttranscriptional gene-silencing phenomena such as cosuppression and RNA interference are associated with the occurrence of small, about 21-23 nt short RNA species homologous to the silenced gene. We here show that the small RNA present in silenced transgenic plants can easily be detected in total RNA isolated according to standard procedures. This will allow for the development of routine and early screenings for the presence of small RNA species and, therefore, gene silencing in transgenic plants. We further demonstrate that the small RNA fraction can be visualized with the SYBR Green II RNA stain, isolated from a gel, labeled and used as a specific probe. Using these approaches, we have fine-mapped the sequences of the GUS gene that are represented in the small RNA fraction of a GUS-silenced tobacco line containing an inverted repeat of the GUS gene. In this tobacco line, the silencing-associated small RNA is a mixture of fragments that cover the 3' two-thirds of the GUS coding region. The 5' coding and the 3' noncoding ends of the GUS mRNA are not represented in the small RNA fraction. The RNA fragments are not likely to be a primary synthesis product of an RNA-dependent RNA polymerase, but rather degradation products from nuclease activity. Surprisingly, RNA isolated from wild-type, untransformed plants showed the presence of a similar-sized small RNA pool. This might indicate the existence of small RNA species from putative endogenous genes that are down regulated by a similar posttranscriptional gene-silencing mechanism. The possibility of isolating and labeling the small RNA pool from wild-type plants will provide a way to identify and study such putative genes.

Fluorescent Dyes↗

PubMed1981

Interaction of the chick oviduct progesterone receptor with deoxyribonucleic acid.

The purified DNA binding component (receptor A) of the chick oviduct progesterone receptor has been analyzed for its ability to bind to the cloned ovalbumin gene and to plasmid DNA of various structural compositions. The rapid equilibrium filter adsorption assay of Riggs et al. [Riggs, A. D., Suzuki, H., & Bourgeois, S. (1970) J. Mol. Biol. 48, 67] has been used to demonstrate high affinity binding of the protein to DNA (Kdiss = 10(-10) M at 50 mM KCl, pH 7.2). Studies of association rates are consistent with equilibrium measurements (t 1/2 = 40-80 min). Association of purified receptor with DNA and the kinetics of the interaction have been verified independently by velocity sedimentation techniques. Direct binding assays were performed with the ovalbumin structural gene (cDNA), the entire natural ovalbumin gene containing seven intervening sequences, and various ovalbumin gene fragments coding for the 5' end of the nuclear precursor RNA, intron-exon junctions, and the 3'-noncoding region of the gene. No DNA-sequence specificity was identified for the binding of the receptor protein to any region of ovalbumin gene DNA. In contrast, the structural integrity of the DNA template greatly affected receptor binding. The poorest affinity was to supercoiled DNA and to blunt end, linear duplex gene fragments. The receptor bound saturably to DNA containing limited nicks but became nonsaturable as nicks were increased. Binding of the protein to double-stranded DNA increased susceptibility of the DNA to digestion by the enzyme S1, a single strand specific nuclease. On the basis of preferential receptor binding to single-stranded DNA, a possible mechanism involving DNA helix destabilization is discussed.

Animals↗

PubMed1999

An internal duplication in the 5' noncoding region of strain H: a bovine viral diarrhoea virus (BVDV) isolated from pigs.

A pig pestivirus isolate, strain H, was characterized by using reverse transcription-PCR (RT-PCR) and direct sequencing of the amplicons. A duplication of 74 nucleotides was found at the 5' terminus of the 5' noncoding (NC) region, which was also found in RNA isolates from tonsils from two other pigs from the same farm. When the duplication was omitted, the 5' NC region showed 97.8% similarity to bovine viral diarrhoea virus (BVDV) strain Korevaar and 94% to BVDV strain Osloss. Furthermore, the rearrangement of the 5' NC region of strain H was maintained after passaging in different cell lines and is not common for ruminant-like pestivirus isolated from pigs. Phylogenetic analysis based on the deduced amino acid sequence of the E2 gene of strain H confirmed the findings of the 5' NC region and show that this strain belongs to the BVDVIb subgroup. These results show for the first time rearrangements in the 5' NC region of a pestivirus.

5' Untranslated Regions↗

PubMed2006

Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus.

Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.

Base Sequence↗

PubMed2002

Hepatitis C and hepatitis B virus infection in different hemodialysis units in Belo Horizonte, Minas Gerais, Brazil.

The prevalence, virological and epidemiological aspects of the hepatitis C virus (HCV) and the hepatitis B virus (HBV) infections vary among hemodialysis patients in different countries. Aiming at analyzing these aspects of HCV and HBV infections in hemodialysis patients in Belo Horizonte, MG, Brazil, we studied three hemodialysis units including 434 patients. Serology was used to detect anti-HCV and HBsAg. Reverse trancriptase nested polymerase chain reaction (RT-nested-PCR) of the 5'-noncoding region was used to detect circulating HCV RNA and restriction fragment length polymorphism analysis for genotyping. Seroprevalence varied from 26.5% to 11.1% for hepatitis C and from 5.9% to 0% for hepatitis B. Risk factors observed for HBV and/or HCV infections were the number of patients per dialysis unit, duration of treatment, number of clinics attended, number of blood units transfused, and lower level scholarity. Alanine aminotransferase levels were altered with a higher frequency in HBV or HCV seropositive patients. Half of ten patients, negative for anti-HCV, had detectable viremia by RT-nested-PCR, indicating that this technique should be used to confirm infections in this group of patients. The HCV genotype 1 was the most frequently observed, followed by the genotype 2, but no correlation was detected between genotype and clinical or epidemiological data.

Adolescent↗

PubMedDate not supplied

In vitro phenotype of SDF1 gene mutant that delays the onset of human immunodeficiency virus disease in vivo.

OBJECTIVE: Inheritance of a mutant allele of the SDF1 gene delays the onset of human immunodeficiency virus type 1 (HIV-1) disease. Because the mutation lies in the 3' untranslated region of the gene, it was suggested that this mutation may upregulate transcription of the gene, resulting in more abundant SDF1, which in turn inhibits T-tropic HIV-1 and delays disease onset. This implies that this segment of SDF1 gene contains a negative regulatory element. We directly tested this hypothesis in vitro. STUDY DESIGN/METHODS: We cloned the wild-type and the mutant SDF1 gene in an HIV-2 gene transfer vector as well as in a baculovirus expression vector. We expressed the cloned genes in human and insect cells in culture and analyzed the abundance of SDF1 RNA by hybridization and protein using antiviral assays. RESULTS: The abundance of SDF1 RNA synthesized by the mutant clone with the mutation in the 3' untranslated region was no different from that synthesized by the wild-type clone in cultured cells. This was the case for both the HIV-2 long terminal repeat (LTR)-directed expression in human cells and baculovirus promoter-directed expression in insect cells. Both clones apparently synthesized SDF1 with equivalent biologic activity. Similar results were obtained for a mutant with the deletion of a GC-rich segment in the 5' untranslated region. CONCLUSIONS: Mutation of the 3' untranslated exon did not affect SDF1 RNA synthesis in vitro. It also did not appear to affect translation of SDF1 RNA. A similar mutational analysis of the 5' noncoding exon suggested that this region also did not regulate SDF1 expression.

3' Untranslated Regions↗

PubMed1988

The nucleocapsid gene of infectious hematopoietic necrosis virus, a fish rhabdovirus.

The complete nucleotide sequence of the infectious hematopoietic necrosis virus (IHNV) nucleocapsid gene has been determined using cDNA clones of genomic and messenger RNAs. Genomic clones were generated by using random DNA oligomers to prime cDNA synthesis and were mapped to their respective locations on the genome by the use of cDNA probes derived from viral mRNAs. Interesting features of the IHNV nucleocapsid gene sequence elucidated by the sequencing of these clones include short homologies with N genes of other rhabdoviruses at the 5' and 3' nontranslated termini of the mRNA, as well as an exceptionally long 5' noncoding region of the mRNA, suggesting a leader RNA may be coupled to the N mRNA. A comparison of the IHNV N protein coding sequence with other rhabdoviral N genes shows some homologies at the amino acid level which indicates the possible evolutionary relationship of these N proteins. The determination of the nucleotide sequences of IHNV genes and intergenic regions will be useful for studying the mechanisms of rhabdoviral transcription and replication.

Amino Acid Sequence↗

PubMed1995

PCR differential display identifies a rat brain mRNA that is transcriptionally regulated by cocaine and amphetamine.

Neuronal plasticity associated with both short- and long-term administration of psychomotor stimulants involves alterations in specific patterns of gene expression. In order to screen for brain region specific mRNAs which are transcriptionally regulated by acute cocaine and amphetamine, PCR differential display was employed. This approach identified a previously uncharacterized mRNA whose relative levels in the striatum are induced four- to fivefold by acute psychomotor stimulant administration. Isolation and characterization of corresponding cDNA clones resulted in complete nucleotide sequence analysis, including prediction of the encoded protein product. Alternate polyA site utilization in the predicted 3' noncoding region results in the appearance of an RNA doublet, approximately 700 and 900 bases in length, following Northern analysis. A presumed alternate splicing event further generates diversity within the transcripts, and results in the presence or absence of an in-frame 39 base insert within the putative protein coding region. As a result, the predicted translation products are either 129 or 116 amino acids in length. A common hydrophobic leader sequence at the amino terminus is present within each predicted polypeptide, suggesting that the protein product is targeted for entry into the secretory pathway. Basal expression of the RNA doublet is limited to neuroendocrine tissues, further implying that the protein product plays a functional role in both neuronal and endocrine tissues.

Amino Acid Sequence↗

PubMed1993

HCV-RNA assay in peripheral blood mononuclear cells in relation to IFN therapy.

Hepatitis C virus RNA (HCV-RNA) was serially assayed in the serum and peripheral blood mononuclear cells (PBMC) of 10 patients with chronic hepatitis C who underwent interferon (IFN) therapy, and whether detection of HCV-RNA from PBMC serves as an index of the response of chronic hepatitis C to IFN therapy was evaluated. HCV-RNA was assayed by reversed transcription and polymerase chain reaction using the 5'-noncoding region as a primer. IFN therapy was effective in 3 patients and ineffective in the other 7 patients. HCV-RNA disappeared from the serum during and immediately after the IFN therapy in all 3 patients in whom the therapy was effective and in 3 of 7 patients in whom the therapy was ineffective. HCV-RNA disappeared from PBMC in all 3 patients in whom the therapy was effective, but PBMC HCV-RNA remained positive in 6 of the 7 patients in whom the therapy was ineffective, and the serum HCV-RNA became positive again in 5 of these 6 patients after 6 months. The disappearance of HCV-RNA from PBMC was associated with long-term stabilization of the serum alanine aminotransferase value, so HCV-RNA assay in PBMC is considered to be useful as a prognostic marker of chronic hepatitis C after IFN therapy.

Adult↗

PubMed1985

Complementarity between ferritin H mRNA and 28 S ribosomal RNA.

We have found an interesting complementarity in sequences of human ferritin H mRNA and 28 S ribosomal RNA. Immediately upstream of the initiating AUG in the ferritin mRNA is a stretch of 67 nucleotides which contains sequences complementary to several regions in 28 S RNA. One such region can form 55 base pairings with the 5' noncoding region of the ferritin H mRNA. Most of the complementarity is due to repeats of CCG in the ferritin mRNA and GGC in the ribosomal RNA. The regions of complementarity in the 28 S RNA appear to be expansion sequences that have arisen in the evolution of eukaryotic ribosomal RNA. We suggest that interaction of ferritin mRNA and 28 S RNA may function to regulate the stability and/or translatability of ferritin mRNA.

Animals↗

PubMed1994

Markers of hepatitis C and B virus infections among blood donors in Ho Chi Minh City and Hanoi, Vietnam.

Blood donors in two cities in Vietnam were tested for markers of hepatitis C virus (HCV) and hepatitis B virus infections. Antibody to HCV was detected by passive hemagglutination with antigens of the second generation in 101 (20.6%) of 491 donors in Ho Chi Minh City; it was detected less frequently (P < 0.001) in donors in hanoi (4 [0.8%] of 499). HCV RNA was tested for in donors with antibody by PCR with nested primers from the 5'-noncoding region and detected in 79 donors in Ho Chi Minh City and 4 donors in Hanoi. HCV RNA was genotyped by PCR with type-specific primers from the core gene. Of 83 HCV carriers from Vietnam, 24 (29%) were infected with HCV of genotype I/1a 19 (23%) were infected with II/1b, 4 (5%) were infected with III/2a, and 2 (2%) were infected with mixed genotypes (I/1a and II/1b); HCV genotypes in the remaining 34 (41%) donors, including all 4 donors in Hanoi, were not classifiable into I/1a, II/2a, IV/2b, or V/3a. Of the 10 isolates with unclassifiable genotypes, 2 showed substantial sequence divergence within the 5'-noncoding region from reported isolates with known genotypes (I/1a to 6a). An analysis of part of the core gene sequence indicated that six of the remaining isolates most likely represented new HCV genotypes. Hepatitis B surface antigen and the corresponding antibody, respectively, were detected in 15 (3.1%) and 234 (47.7%) donors in Ho Chi Minh City as well as 15 (3.0%) and 248 (49.7%) donors in Hanoi. These results indicate an extensive spread of HCV among Ho Chi Minh City donors and HCV of novel genotypes in vietnam.

Adult↗

PubMed2002

A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco.

Two major classes of small noncoding RNAs have emerged as important regulators of gene expression in eukaryotes, the short interfering RNAs (siRNAs) associated with RNA silencing and endogenous micro-RNAs (miRNAs) implicated in regulation of gene expression. Helper component-proteinase (HC-Pro) is a viral protein that blocks RNA silencing in plants. Here we examine the effect of HC-Pro on the accumulation of siRNAs and endogenous miRNAs. siRNAs were analyzed in transgenic tobacco plants silenced in response to three different classes of transgenes: sense-transgenes, inverted-repeat transgenes, and amplicon-transgenes. HC-Pro suppressed silencing in each line, blocking accumulation of the associated siRNAs and allowing accumulation of transcripts from the previously silenced loci. HC-Pro-suppression of silencing in the inverted-repeat- and amplicon-transgenic lines was accompanied by the apparent accumulation of long double-stranded RNAs and proportional amounts of small RNAs that are larger than the siRNAs that accumulate during silencing. Analysis of these results suggests that HC-Pro interferes with silencing either by inhibiting siRNA processing from double-stranded RNA precursors or by destabilizing siRNAs. In contrast to siRNAs, the accumulation of endogenous miRNAs was greatly enhanced in all of the HC-Pro-expressing lines. Thus, our results demonstrate that accumulation of siRNAs and miRNAs in plants can be differentially regulated by a viral protein. The fact that HC-Pro affects the miRNA pathway raises the possibility that this pathway is targeted by plant viruses as a means to control gene expression in the host.

Glucuronidase↗

PubMed1993

[Importance of primer selection in 5'NC region for the detection of hepatitis C virus RNA by polymerase chain reaction].

We compared two primer sets (A: 167bp, B: 269bp) derived from highly conserved domains within the 5' noncoding region (5'NC) of the hepatitis C virus (HCV) genome for their ability to detect HCV-RNA in a nested cDNA polymerase chain reaction assay (nested-PCR) in sera from 31 patients suspected of having HCV infection. Seventeen (54%) of 31 patients were positive for HCV-RNA with both primer sets. Using primer set A, 14(93%) of 15 samples with positive and 3(19%) of 16 samples with negative anti-HCV antibody test gave positive results for HCV-RNA. With primer set B, 15(100%) of 15 antibody positive samples and 2(13%) of 16 negative samples were positive for HCV-RNA. One antibody negative sample from a patient with alcoholic liver cirrhosis was positive for HCV-RNA only with primer set A. Another sample with positive antibody test, from a patient with chronic renal failure, was positive for HCV-RNA only with primer set B. A combination of more than one set of primers directed to the highly conserved 5'NC region, as well as proper selection of the exact nucleotide sequences, are important in improving the detection rate of HCV-RNA by PCR in serum of infected patients.

Base Sequence↗