Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “viral noncoding RNA”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 505 records · Page 28Linked to original sources
PubMed2001

Deletion or substitution of the aphthovirus 3' NCR abrogates infectivity and virus replication.

The 3' noncoding region (NCR) of the genomic picornaviral RNA is believed to contain major cis-acting signals required for negative-strand RNA synthesis. The 3' NCR of foot-and-mouth disease virus (FMDV) was studied in the context of a full-length infectious clone in which the genetic element was deleted or exchanged for the equivalent region of a distantly related swine picornavirus, swine vesicular disease virus (SVDV). Deletion of the 3' NCR, while maintaining the intact poly(A) tail as well as its replacement for the SVDV counterpart, abrogated virus replication in susceptible cells as determined by infectivity and Northern blot assays. Nevertheless, the presence of the SVDV sequence allowed the synthesis of low amounts of chimeric viral RNA at extended times post-transfection as compared to RNAs harbouring the 3' NCR deletion. The failure to recover viable viruses or revertants after several passages on susceptible cells suggests that the presence of specific sequences contained within the FMDV 3' NCR is essential to complete a full replication cycle and that FMDV and SVDV 3' NCRs are not functionally interchangeable.

3' Untranslated Regions↗
PubMed1989

Differences in replication of attenuated and neurovirulent polioviruses in human neuroblastoma cell line SH-SY5Y.

A base change from C to U at position 472 of the 5' noncoding region of the poliovirus genome is known to be a major determinant of attenuation in the P3/Sabin vaccine strain. To determine the biochemical basis for the attenuated phenotype imparted by this mutation, a cell line in which replication of neurovirulent and attenuated viruses could be distinguished was identified. A pair of P3/Sabin-P2/Lansing viral recombinants that differ only at position 472 was used; the viruses replicated equally well in HeLa cells, but the virus with a U at base 472 was attenuated in mice. In the human neuroblastoma cell line SH-SY5Y, recombinants with a U at base 472 replicated to approximately 10-fold-lower titers than did neurovirulent viruses with a C at this position. Analysis of viral RNA and protein synthesis indicated that translation of the attenuated viral RNA was specifically reduced in SH-SY5Y cells.

HeLa Cells↗
PubMed1997

Chronic variant of myocarditis associated with hepatitis C virus infection.

BACKGROUND: Although molecular biological studies suggest a pathogenic link between enterovirus infection and dilated cardiomyopathy (DCM), the frequency of detection of enteroviral RNA is not consistently high in myocardial tissue from patients with DCM. A recent study has suggested that hepatitis C virus (HCV) may also be involved in the development of DCM. METHODS AND RESULTS: We performed genomic analysis for HCV in three patients with chronic active myocarditis. In all three patients, serum aminotransferase activities remained within normal ranges until the terminal stage of heart failure. At necropsy, all three livers showed evidence of tissue damage caused by chronic congestion, and one liver had evidence of chronic hepatitis. Routinely processed, paraffin-embedded tissue blocks of myocardium and liver were analyzed. Renal specimens were also analyzed to exclude the possibility of myocardial contamination with HCV material from the circulating blood. RNA extracted from the heart, liver, and kidney was subjected to strand-specific reverse transcription and amplified by semi-nested polymerase chain reaction. The target nucleotide sequence was a 178-bp fragment of the highly conserved 5'-noncoding region. Both positive- (genomic) and negative-strand RNA (replicative intermediates) were present in myocardial and liver tissue samples from all three patients. However, negative-strand RNA was undetectable in renal tissue from one patient. CONCLUSIONS: These findings suggest that HCV replicated in myocardial tissue of these patients with myocarditis. Thus, HCV infection may contribute to the development of this unusual form of myocarditis.

Chronic Disease↗
PubMed1991

Simian immunodeficiency virus (SIVmac) exhibits complex splicing for tat, rev, and env mRNA.

The simian immunodeficiency virus (SIV) is a T-lymphotropic lentivirus associated with a fatal AIDS-like disease in rhesus macaques. SIV has a complex genome encoding virion structural proteins, transactivators, and accessory genes. From lymphoid cells chronically infected with a biologically active molecular clone of SIV, SIVmac1A11, the polymerase chain reaction technique has been used to selectively amplify transcripts for viral transactivators and the envelope gene. Three species of mRNA encoding only rev, and three mRNA encoding both rev and tat were identified by nucleotide sequence analysis. They differed in the splice acceptor sites utilized upstream of the first coding exon, in the presence or the absence of noncoding exons between the major splice donor at the LTR and the splice acceptor at the first coding exons, and in the splicing pattern between the coding exons. Alternate splice acceptors were utilized between the coding exons of tat and rev, but the altered tat proteins did not differ in their ability to transactivate the SIV-LTR. The splicing for env mRNA is more complex than previously reported. Both singly and multiply spliced transcripts exist for env mRNA, and the same splice acceptor site is utilized by both rev and env mRNA.

Amino Acid Sequence↗
PubMed1978

Nucleotide sequence of turnip yellow mosaic virus coat protein mRNA.

The primary structure of the coat protein messenger RNA of turnip yellow mosaic virus is presented. This sequence is the first complete nucleotide sequence of the coat protein messenger of a plant virus to be reported. The coding region, consisting of 567 nucleotides, is flanked by a 5' noncoding region of 19 nucleotides (not including the initiation codon and the cap structure) and by a 3' noncoding region of 109 nucleotides (including the termination signal). The coat protein mRNA has a base composition identical to that of the genome RNA with, in particular, the same high content in cytosine (38%). The codons that govern the incorporation of amino acids into the coat protein are nonrandomly utilized: is greater than 50% of the time the third base of the codons used is a cytosine. This pattern of codon preference is particularly marked for Leu, lle Val, Thr and Cys.

Base Sequence↗
PubMed1986

Epidermodysplasia verruciformis-associated human papillomavirus 8: genomic sequence and comparative analysis.

Human papillomavirus (HPV) 8 induces skin tumors which are at high risk for malignant conversion. The nucleotide sequence of HPV8 has been determined and compared to sequences of papillomaviruses with different oncogenic potential. The general organization of the HPV8 genome is similar to that of other types. Highly conserved, genus-specific sequences were found in open reading frames (ORFs) E1, E2, and L1. In ORFs E6, E7, and L2, HPV8 is more distantly related, but it was possible to differentiate subgenera in which HPV8 belonged to the HPV1-cottontail rabbit papillomavirus group. Sequences within ORF E4 and part of ORF L2 are rather type specific. HPV8 stands out by several unique features: the considerably reduced size of the noncoding region (397 base pairs), with a seemingly low potential for forming complex secondary structures; a cluster of putative promoter elements in the 3' half of ORF E1; an RNA polymerase III promoter-like sequence close to the C terminus of ORF E2; and of particular interest, the homology between the putative protein encoded by ORF E4 and the Epstein-Barr virus nuclear antigen 2 protein, which may reflect similar mechanisms in virus-mediated transformation.

Amino Acid Sequence↗
PubMed1988

Translational efficiency of poliovirus mRNA: mapping inhibitory cis-acting elements within the 5' noncoding region.

Poliovirus mRNA contains a long 5' noncoding region of about 750 nucleotides (the exact number varies among the three virus serotypes), which contains several AUG codons upstream of the major initiator AUG. Unlike most eucaryotic mRNAs, poliovirus does not contain a m7GpppX (where X is any nucleotide) cap structure at its 5' end and is translated by a cap-independent mechanism. To study the manner by which poliovirus mRNA is expressed, we examined the translational efficiencies of a series of deletion mutants within the 5' noncoding region of the mRNA. In this paper we report striking translation system-specific differences in the ability of the altered mRNAs to be translated. The results suggest the existence of an inhibitory cis-acting element(s) within the 5' noncoding region of poliovirus (between nucleotides 70 and 381) which restricts mRNA translation in reticulocyte lysate, wheat germ extract, and Xenopus oocytes, but not in HeLa cell extracts. In addition, we show that HeLa cell extracts contain a trans-acting factor(s) that overcomes this restriction.

Animals↗
PubMed1995

An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region.

Translation of the human hepatitis C virus (HCV) RNA genome occurs by a mechanism known as "internal ribosome entry." This unusual strategy of translation is employed by naturally uncapped picornaviral genomic RNAs and several cellular mRNAs. A common feature of these RNAs is a relatively long 5' noncoding region (NCR) that folds into a complex secondary structure harboring an internal ribosome entry site (IRES). Evidence derived from the use of dicistronic expression systems, combined with an extensive mutational analysis, demonstrated the presence of an IRES within the HCV 5'NCR. The results of our continued mutational analysis to map the critical structural elements of the HCV IRES has led to the identification of a pseudoknot structure upstream of the initiator AUG. The evidence presented in this study is based upon the mutational analysis of the putative pseudoknot structure. This is further substantiated by biochemical and enzymatic probing of the wild-type and mutant 5'NCR. Further, the thermodynamic calculations, based upon a modified RNAKNOT program, are consistent with the presence of a pseudoknot structure located upstream of the initiator AUG. Maintenance of this structural element is critical for internal initiation of translation. The pseudoknot structure in the 5'NCR represents a highly conserved feature of all HCV subtypes and members of the pestivirus family, including hog cholera virus and bovine viral diarrhea virus.

Base Sequence↗
PubMed1998

Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase.

The mRNA cap structure is synthesized by a series of reactions catalyzed by capping enzyme and mRNA (guanine-7-)-methyltransferase. mRNA (guanine-7-)-methyltransferase catalyzes the methylation of GpppN- at the guanine N7 position, which is an essential step for gene expression in eukaryotic cells. Here we isolated three human cDNAs encoding mRNA (guanine-7-)-methyltransferase termed hCMT1a, hCMT1b and hCMT1c. hCMT1a and hCMT1b encode 476 and 504 amino acids, respectively, and differ only at the region coding for the C-terminal portion of the enzyme after amino acid residue 465. The third cDNA hCMT1c seems to encode the same polypeptide as hCMT1a, however, the 3'-noncoding region of hCMT1c contains sequences corresponding to part of the C-terminal coding and noncoding regions of hCMT1b thus consisting of a mosaic of hCMT1a and hCMT1b. RT-PCR showed that all 3 types of mRNAs were expressed in every tissue examined. Comparison of the deduced amino acid sequences with those of other viral and cellular enzymes showed the regions which are highly conserved among mRNA (guanine-7-)-methyltransferases. The recombinant hCMT1a expressed in E. coli exhibited mRNA (guanine-7-)-methyltransferase activity. On the other hand, neither mRNA (guanine-7-)-methyltransferase nor mRNA (nucleoside-2'-O-)-methyltransferase activity was detected with the recombinant hCMT1b protein. Although the biological significance of the expression of these three mRNA (guanine-7-)-methyltransferase mRNA species remains unknown at present, the nucleotide sequences suggest that they are produced by alternative RNA splicing.

Amino Acid Sequence↗
PubMed1992

Mechanism of attenuation of a chimeric influenza A/B transfectant virus.

The ribonucleoprotein transfection system for influenza virus allowed us to construct an influenza A virus containing a chimeric neuraminidase (NA) gene in which the noncoding sequence is derived from the NS gene of influenza B virus (T. Muster, E. K. Subbarao, M. Enami, B. P. Murphy, and P. Palese, Proc. Natl. Acad. Sci. USA 88:5177-5181, 1991). This transfectant virus is attenuated in mice and grows to lower titers in tissue culture than wild-type virus. Since such a virus has characteristics desirable for a live attenuated vaccine strain, attempts were made to characterize this virus at the molecular level. Our analysis suggests that the attenuation of the virus is due to changes in the cis signal sequences, which resulted in a reduction of transcription and replication of the chimeric NA gene. The major finding concerns a sixfold reduction in NA-specific viral RNA in the virion, causing a reduction in the ratio of infectious particles to physical particles compared with the ratio in wild-type virus. Although the NA-specific mRNA level is also reduced in transfectant virus-infected cells, it does not appear to contribute to the attenuation characteristics of the virus. The levels of the other RNAs and their expression appear to be unchanged for the transfectant virus. It is suggested that downregulation of the synthesis of one viral RNA segment leads to the generation of defective viruses during each replication cycle. We believe that this represents a general principle for attenuation which may be applied to other segmented viruses containing either single-stranded or double-stranded RNA.

Animals↗
PubMed1994

Complete nucleotide sequence and genomic organization of the Aedes albopictus parvovirus (AaPV) pathogenic for Aedes aegypti larvae.

We have cloned the replicative form of the Aedes albopictus parvovirus (AaPV) genome and determined the complete sequence of the viral strand. The sequence is 4176 nucleotides (nt) in length. The first 134 nt at the 3' end and the terminal 182 nt at the 5' end of the viral (minus) strand can both generate by folding and annealing of complementary sequences a typical terminal T-shaped structure although they differ in their sequence. Three large open reading frames (ORFs), each one in a different frame, are present between map units (mu) 8.0 and 87.6 on the complementary (plus) strand. The left, mid (located within the left ORF), and right ORFs have potential coding capacities of 95, 41, and 40 kDa, respectively. Two potential promoters were found upstream from the left and right ORFs, at mu 7.2 and mu 60.0, respectively. Computer search for sequence homologies suggests that the left ORF very likely encodes the nonstructural NS-1 protein since it contains the highly conserved NTP-binding amino acid (aa) domain (GKRN sequence) of all parvoviruses. Comparison with other invertebrate and vertebrate parvoviruses revealed that the AaPV genome shares 77.3% nt sequence homology and between 73 and 78% aa sequence homologies with the Aedes aegypti densonucleosis virus (Aedes DNV). Organization of both genomes was similar except that no potential ORF was found on the minus strand of AaPV. The difference of 167 nt in length between AaPV and Aedes DNV (4009 nt) genomes is due to additional noncoding sequences located between the internal coding region and the terminal palindromes in the AaPV genome. No significant homology was found between AaPV and the two other insect parvoviruses sequenced so far, the Bombyx mori DNV (BmDNV) and the Junonia coenia DNV (JcDNV).

Aedes↗
PubMed1986

Transcriptional control signals of a herpes simplex virus type 1 late (gamma 2) gene lie within bases -34 to +124 relative to the 5' terminus of the mRNA.

The cis-acting DNA sequences required for regulated expression of a herpes simplex virus type 1 (HSV-1) late (gamma 2) gene were studied by using viruses containing specific deletions in the 5' transcribed noncoding and upstream regions of the HSV-1 glycoprotein C (gC) gene, a model gamma 2 gene. Nine mutant viruses which had variable 5' and 3' deletions within bases -569 to +124 relative to the 5' terminus of the gC mRNA were isolated. The mutants were isolated by a simple in situ hybridization screening procedure not requiring any prior selective pressure for or against expression of the gC gene. Analysis of RNA extracted from cells infected with individual mutants showed that the DNA sequences required for regulated expression of this gamma 2 gene lay within bases -34 to +124. This 158-base-pair fragment was sufficient to confer accurate and quantitative expression of gC mRNA and to maintain the stringent requirement on viral DNA replication for expression of this gene. Moreover, it was found that sequences located between -34 and +14 contained signals essential for expression of gC. To determine whether the -34 to +124 sequences would function as a gamma 2 promoter when moved to another region of the HSV-1 genome, the 158-base-pair fragment was substituted for the normal thymidine kinase promoter-regulatory sequences in the thymidine-kinase gene locus. Transcription of this chimeric gene was regulated as a gamma 2 gene in that its expression in infected cells was dependent on viral DNA synthesis. The only recognizable consensus sequence upstream of the transcription initiation site for this gene was the TATAAA sequence at -30.

Animals↗
PubMed1990

Genomic regions of neurovirulence and attenuation in Theiler murine encephalomyelitis virus.

Full-length cDNA clones of two Theiler murine encephalomyelitis virus (TMEV) strains, one highly virulent and the other less virulent, were constructed in the bacterial plasmid pGEMR-3. Transfection of BHK-21 cells with RNA transcribed from these cDNAs yielded progeny viruses with the exact in vitro growth phenotype and mouse neurovirulence pattern of the respective parental virus strains. RNA transcripts derived from recombinant chimeras constructed by exchanging corresponding genomic regions [5' noncoding, leader/P1 (L/P1), P2, P3, and 3' noncoding] between the parental cDNAs were infectious and enabled analysis of the growth characteristics in vitro and mouse neurovirulence of the chimeras. A correlation was found between plaque size and temperature sensitivity and the origin of the L/P1 region. Neurovirulence mapped primarily to the L/P1 region encoding the leader and coat proteins. Depending on parental origin, the 5' noncoding region either influenced virus attenuation or augmented virulence.

Animals↗
PubMed2001

Transcription activation of polyadenylated nuclear rna by rta in human herpesvirus 8/Kaposi's sarcoma-associated herpesvirus.

Human herpesvirus 8 (HHV-8) (also known as Kaposi's sarcoma-associated herpesvirus) encodes a novel noncoding polyadenylated nuclear (PAN) RNA (also known as T1.1 or nut-1) during the early phase of lytic replication. PAN RNA is the most abundant transcript of HHV-8, comprising 80% of total poly(A)-selected transcripts in HHV-8-infected cells during lytic replication. We directly measured the abundance of PAN RNA by visualizing 1.1- to 1.2- kb PAN RNA in an ethidium bromide-stained gel from poly(A)-selected RNA. We further pursued the mechanisms by which PAN RNA expression is induced to such high levels. rta, an immediate-early gene of HHV-8, is a transactivator that is sufficient and necessary to activate lytic gene expression in latently infected cells. Ectopic expression of Rta was previously shown to induce PAN RNA expression from the endogenous viral genome and activate the PAN promoter in a reporter system. Here, we have identified the Rta-responsive element (RRE) in the PAN promoter. Deletion analysis revealed that the RRE is present in a region between nucleotides -69 and -38 of the PAN promoter. A promoter construct containing the 69 nucleotides upstream of the transcription start site of the PAN promoter was activated by Rta in the absence or presence of the HHV-8 genome. Rta activated the PAN promoter up to 7,000-fold in 293T cells and 2,000-fold in B cells. Electrophoretic mobility shift assays demonstrated that Rta formed a highly stable complex with the RRE of the PAN promoter. Our study suggests that Rta can induce PAN RNA expression by direct binding of Rta to the RRE of the PAN promoter. This study has highlighted an important mechanism controlling PAN RNA expression and also provides a model system for investigating how Rta transactivates gene expression during lytic replication.

Animals↗
PubMed1998

Single-step reverse transcription-polymerase chain reaction for the detection of hepatitis C virus RNA.

We developed a novel single-step reverse transcription-polymerase chain reaction (RT-PCR), which is equal in sensitivity and specificity to RT-nested PCR, based on both reverse transcriptase and Taq DNA polymerase working efficiently under single buffer reaction conditions. Using in vitro synthesized hepatitis C virus (HCV) RNA, it was demonstrated that 10-100 copies of HCV RNA could be detected with a set of primers that amplify a 144 base-pair sequence unique to the 5'-noncoding region of HCV RNA. Furthermore, this method was successfully performed on serum and liver biopsy specimens obtained from patients with chronic hepatitis C. In addition, HCV RNA from in vitro HCV-infected MT-2C cells, which supported HCV replication, was also detected by this method. The method is anticipated to improve the detection of small amounts of RNA, such as that of HCV, promoting both labor savings and the prevention of carry-over contamination.

Hepacivirus↗
PubMed1995

Demonstration and distribution of HCV RNA sequences by in situ hybridization and HCV-related proteins by immunohistochemistry in the liver tissue of patients with chronic HCV infection.

Nonisotopic in situ cytohybridization of HCV RNA was attempted in liver specimens from 12 chronically hepatitis C virus (HCV) infected patients. Oligonucleotides deduced from 5'-noncoding and core regions of the HCV genome were labeled with digoxigenin and used on paraformaldehyde-fixed frozen liver sections. The hybrids were visualized immunohistochemically with alkaline phosphatase-conjugated anti-digoxigenin and alkaline phosphatase substrate. These findings were correlated with the results of tissue immunohistochemistry for HCV antigens identified with specific mouse monoclonal antibodies developed against c22-3 antigen (Ag), a core-encoded protein, and c100-3 Ag, a NS4-encoded protein, and histologic assessment of each liver. HCV RNA detected in the above assay was predominantly cytoplasmic; it was detected in all 12 patients and in none of the controls. Tissue HCV RNA was associated with the presence of cytoplasmic (c100-3 Ag) and membrane (c22-3 Ag) expression of viral proteins in all 9 patients with histological evidence of chronic progressive liver disease as judged by the presence of piecemeal necrosis, and lobular and portal tract inflammation. Despite the presence of abundant HCV RNA, none of 3 patients without histological evidence of chronic liver disease showed intrahepatocyte expression of viral proteins. These findings support the view that tissue HCV antigens are markers of progressive damage and demonstrate that active liver disease does not occur without such markers. It is proposed that synthesis of viral proteins and membrane accumulation of c22-3 Ag may be involved in the pathogenesis of hepatocyte injury in chronic hepatitis C infection.

Adult↗
PubMed1978

A nuclear extract of Xenopus laevis oocytes that accurately transcribes 5S RNA genes.

Xenopus 5S RNA genes in recombinant form with the plasmid pMB9 are transcribed accurately when added to a supernatant fraction obtained from disrupted nuclei of Xenopus laevis oocytes. After an initial 30 min lag period, the rate of synthesis of 5S RNA is constant for at least an hour and synthesis is still detected after 18 hr. As much as 40% of the total RNA synthesized from the recombinant DNA used in these experiments can be 5S RNA. The coding strand of the 5S RNA genes is transcribed at a rate 10 to 15 times greater than the noncoding strand. Plasmid and spacer DNA, however, are also transcribed. What fraction of total RNA synthesized is 5S RNA is strongly affected by DNA concentration, ionic strength and MgCl2 concentration. Inhibition of transcription by intermediate concentrations of alpha-amanitin demonstrates that RNA polymerase III transcribes at least 90% of all RNA synthesized. Adenovirus 2 DNA is also transcribed in the nuclear supernatant by RNA polymerase III. Approximately 15% of the total RNA synthesized migrates in an acrylamide gel as a band of 5.5S RNA and has been identified as virus-associated RNA1 by its oligonucleotide fingerprint.

Animals↗
PubMed1984

Adenovirus tripartite leader sequence enhances translation of mRNAs late after infection.

A series of adenovirus type 5 variants was constructed to probe the function of the tripartite leader sequence, a 200-nucleotide, 5' noncoding sequence carried on the majority of late viral mRNAs. Recombinant plasmids were constructed that carried the major late transcriptional control region followed by portions of the tripartite leader sequence fused to the E1A coding region. These modified E1A genes were then rebuilt into intact viral chromosomes, replacing the corresponding wild-type region. The leader segments had no effect on the translation of E1A mRNAs early after infection, but the tripartite leader significantly enhanced (5-fold) the efficiency with which the mRNAs were translated late after infection.

Adenoviruses, Human↗