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Results for “RNA, Antisense”

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At least 19 recordsLinked to original sources
PubMed1991

Inhibition of heterologous strains of HIV by antisense RNA.

Antisense RNA can inhibit the expression of messenger RNAs (mRNAs) to which they are complementary by a variety of mechanisms and might provide the basis for antiviral therapies of high selectivity. In a previous study of six retrovirally expressed antisense RNAs targeted to HIV-1IIIB, we found that two significantly reduced HIV-1IIIB replication. Here we test the degree to which this inhibitory effect tolerates the natural variation found in the nucleotide sequence of different strains of HIV-1. We show that the longer of the two inhibitory antisense RNAs (600 bases) inhibits replication of HIV strains RF, MN and SF2 to at least as great an extent as it does the homologous strain. In contrast, the shorter (71 bases) does not inhibit replication of the heterologous strains. An examination of the predicted positions of the mismatches in the duplexes formed between the IIIB antisense RNAs and the mRNAs of heterologous strains suggests that one requirement of an inhibitory antisense RNA is that it can form a perfect duplex with its target mRNA of at least some 51-64 base-pairs. Although the observations presented here are not definitive proof of this, they are reminiscent of the structural requirements deduced for the double-stranded RNA-mediated induction of interferon and the activation of interferon-induced 2', 5'-oligo(A) synthetase and protein kinase. We tested the ability of antisense RNA to inhibit HIV replication in Jurkat, CEM, U937 and HeLa-T4 cells. The level of inhibition of HIV-1IIIB replication varied according to the cell line in which it was expressed, but in all cases was significant.

Animals↗
PubMed1997

Identification and location of human papillomavirus type 16 antisense early promoter and characterisation of antisense RNA.

Antisense RNA sequences of various regions of human papillomavirus type 16 (HPV 16) were previously found in a number of cervical lesions, but the viral or cellular promoter has not been identified. HPV 16 E7 oncogene antisense transcripts expressed from an antisense promoter in viral DNA were found in the present study by RNase protection assays for total and cytoplasmic RNA. The antisense promoter for these transcripts was located within HPV 16 nt 4030-4230 by deletion analyses. The results also suggested that most of the antisense RNA was relatively short. The antisense promoter of HPV 16 was functional for expression of antisense RNA of a heterologous gene. Antisense-sense double-stranded E7 RNA was detected, and the sense RNA of this duplex was apparently inefficient for splicing or cleavage/poly(A) addition. These results show that HPV 16 can produce early region antisense RNA, which is from a promoter within a defined region of the viral genome. The possible importance of these transcripts for the regulation of episomal HPV 16 gene expression in infected and premalignant lesions and the possible importance of their deregulation for expression in malignant lesions are discussed.

Animals↗
PubMed1990

Inhibition of human immunodeficiency virus replication in cell culture by endogenously synthesized antisense RNA.

Antisense RNA, which has a sequence complementary to mRNA, may provide the basis for antiviral therapies of high selectivity. We have explored the inhibitory effect of six antisense RNAs upon the replication of human immunodeficiency virus (HIV) in cell culture. We chose regions of the HIV genome to test whether sequences required for splicing or for translation initiation were more susceptible to antisense RNA interference. Our results suggest that inhibitory antisense RNAs contain sequences complementary to the AUG initiation codon of the tat gene and have a comparatively low tendency to form intramolecular base pairs which would interfere with intermolecular duplex formation. Inhibition can be substantial (over 70%) but is transient. Transience does not result from mutation of the input virus. Inhibition was not a consequence of the induction of interferon by antisense RNA-mRNA duplex formation. Our results suggest that at least part of the inhibitory effect is at the posttranscriptional level.

Base Sequence↗
PubMed2002

Genomic analysis using conditional phenotypes generated by antisense RNA.

Antisense technology has been widely used to regulate gene expression. A tetracycline (tet)-regulated antisense-RNA-expressing system has been developed and used to downregulate chromosomally derived genes expressed in Staphylococcus aureus. This downregulation subsequently provides an evaluation of the virulence factor and drug targets. The regulated antisense RNA library allows for genome-wide analyses of the functions of staphylococcal gene products for growth in culture and survival during infection. Moreover, this antisense RNA technology may provide a key tool to identify mechanisms of novel antibacterial compound action.

Drug Resistance, Bacterial↗
PubMed1993

A switch in translation mediated by an antisense RNA.

Antisense RNAs regulate expression of target genes in a variety of ways--transcription termination, translation initiation, and mRNA stability. We describe a case in which the target gene encodes two polypeptides, and antisense RNA causes a switch in its translation by selectively inhibiting synthesis of one of the polypeptides. Bacteriophage P22 is a temperate Salmonella phage; in the prophage state it expresses only a handful of its genes. One of these genes, sieB, aborts the lytic development of some phages. P22 itself is insensitive to the lethal effect of SieB because it harbors a determinant called esc. We show that the sieB gene encodes two polypeptides--SieB, which is the exclusion protein, and Esc, which is a truncated version of SieB that inhibits its action. Superinfecting P22 synthesizes an antisense RNA, sas, that inhibits synthesis of SieB but allows continued synthesis of Esc, thus allowing P22 to bypass SieB-mediated exclusion. This translational switch induced by sas RNA is essential to vegetatively developing P22; a mutation that prevents this switch causes P22 to commit SieB-mediated suicide. Finally, we show that P22's Esc allows it to circumvent the SieB-mediated exclusion system of bacteriophage lambda.

Bacteriolysis↗
PubMed1995

The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics.

Replication of the ColE1 group plasmids is kinetically regulated by the interaction between plasmid-encoded primer RNA II and antisense RNA I. The binding is dependent on alternative RNA II conformations, formed during the transcription, and effectively inhibits the primer function within some time interval. In this paper, the folding pathways for the wild type and copy number mutants of ColE1 RNA II are studied using simulations by a genetic algorithm. The simulated pathways reveal a transient formation of a metastable structure, which is stabilized by copy number mutations. The folding kinetics of the proposed conformational transitions is calculated using a model of a multistep refolding process with elementary steps of double-helical stem formation or disruption. The approximation shows that the lifetime of the metastable structure is relatively long and is considerably increased in the mutants, resulting in a delay of the formation of the stable RNA II structure, which is the most sensitive to the inhibition by the antisense RNA I. Thus the effect of copy number mutations can be interpreted as a compression of the time window of effective inhibition due to an increased time spent by the RNA II in the metastable state. The implications of metastable foldings in RNA functioning are discussed.

Algorithms↗
PubMed1997

The design of antisense RNA.

Antisense nucleic acids comprise short-chain synthetic oligonucleotides, often oligodeoxyribonucleotides (ODN) of less than approximately 30 nucleotides and substantially longer sequences formed by ribonucleic acids (RNA). Both groups differ with respect to several properties, including their generation, the mode of delivery, and their structure-function relationship. Long-chain antisense RNA transcribed in vitro or endogenously from recombinant genes fold into three-dimensional structures. The pairing reaction with their complementary target strand occurs via largely unknown annealing mechanisms and, depending on the phylogenetic cellular background, in different cellular compartments. The annealing pathway is influenced by a variety of biologic and biochemical parameters that are as yet poorly understood. However, the basal biochemical mechanisms underlying the relationship between RNA structure and efficient annealing could allow one to derive more general rules for the design of in vivo effective antisense RNA in a way that is not dependent on specific cell types. Here, some of the criteria are discussed that are currently thought to have major impact on the design of long-chain antisense RNA.

Animals↗
PubMed1989

Ribozyme, antisense RNA, and antisense DNA inhibition of U7 small nuclear ribonucleoprotein-mediated histone pre-mRNA processing in vitro.

A comparative analysis of ribozyme, antisense RNA, and antisense DNA inhibitors of the in vitro small nuclear ribonucleoprotein U7-dependent histone pre-mRNA processing reaction was performed. RNA molecules complementary to the U7 sequence inhibited in vitro processing of histone pre-mRNA at a sixfold excess over U7. Single-stranded DNA complementary to the entire U7 sequence inhibited the reaction at a 60-fold excess over U7, while a short, 18-nucleotide DNA molecule complementary to the 5' end of U7 inhibited the processing reaction at a 600-fold excess. A targeted ribozyme was capable of specifically cleaving the U7 small nuclear ribonucleoprotein in a nuclear extract and inhibited the U7-dependent processing reaction, but in our in vitro system it required a 1,000-fold excess over U7 for complete inhibition of processing.

Animals↗
PubMed1987

Stable and heritable inhibition of the expression of nopaline synthase in tobacco expressing antisense RNA.

Antisense nopaline synthase (nos) (D-nopaline synthase; EC 1.5.1.19) RNA is stably expressed from the cauliflower mosaic virus 35S promoter in transformed tobacco plants. The expression of a previously introduced wild-type nos gene is inhibited by the antisense RNA, with less nos enzyme activity detected (by a factor of 8-50) depending on the tissue analyzed. The steady-state levels of nos mRNA are reduced in the presence of the antisense RNA, implying that mRNA degradation is probably the main mode of action for the decrease in expression in this system. The antisense RNA-expressing gene and its inhibition of nos expression are shown to be heritable, demonstrating that it is a potentially useful method for the modification of phenotype.

Journal Article↗
PubMed1996

Onset of C. elegans gastrulation is blocked by inhibition of embryonic transcription with an RNA polymerase antisense RNA.

Cleavage and gastrulation initiation in Caenorhabditis elegans embryos are characterized by an invariant temporal and spatial pattern of cell divisions and cell movements. Although bulk embryonic transcription does not begin until gastrulation onset, some transcription can be detected as early as the 4-cell stage. To determine whether any early transcripts are required for normal cleavage-stage patterning, we blocked transcription in embryos by injecting hermaphrodite parental gonads with RNA antisense to the ama-1 gene, which encodes the large subunit of RNA polymerase II. This treatment prevented the expression of a reporter gene driven by an early embryonic promoter but did not detectably perturb the maternally controlled segregation of the germ line P granules or the pattern of cell division through the first four cleavages. In the fifth cell cycle, however, the two endodermal precursor (E) cells divided early and abnormally and failed to initiate gastrulation. The embryos arrested between the sixth and seventh cell cycles with less than 100 cells. These results indicate that embryonically transcribed gene products are required for gastrulation initiation. They also demonstrate the efficacy of a method for blocking embryonic transcription that may be useful in other organisms.

Animals↗
PubMed1994

YBR1012 an essential gene from S. cerevisiae: construction of an RNA antisense conditional allele and isolation of a multicopy suppressor.

The gene YBR1012 was identified during the systematic sequencing of chromosome II of the yeast Saccharomyces cerevisiae. We have inactivated the gene and shown that it is essential for cellular viability. Using antisense RNA technology we have constructed a conditional allele, expression of the antisense RNA strongly inhibits growth. To our knowledge this is the first successful use of antisense RNA technology in S. cerevisiae. Comparison of the deduced ybr1012p sequence with the data banks revealed the presence of a putative phosphatidylinositol kinase domain and a strong homology to the Schizosaccharomyces pombe rad3p. These results suggest that ybr1012p may be involved in signal transduction, possibly related to the control of replication and/or DNA damage repair. The link with DNA damage repair was reinforced by the isolation of the DUN1 gene as a multicopy suppressor of the YBR1012 deletion.

Alleles↗
PubMed1987

Antisense RNA inactivation of myosin heavy chain gene expression in Dictyostelium discoideum.

The role of myosin in the contraction of striated muscle cells is well known, but its importance in nonmuscle cells is not yet clear. The function of myosin in Dictyostelium discoideum has been investigated by isolating cells which specifically lack myosin heavy chain (MHC A) protein. Cells were transformed with a vector encoding RNA complementary to mhcA messenger RNA (antisense RNA). Stable transformants have a dramatic reduction in the amount of MHC A protein, grow slowly, and generate giant multinucleated progeny, indicating an impairment in cytokinesis. Surprisingly, the cells adhere to surfaces, extend pseudopods and are capable of ameboid locomotion. The developmental sequence that is initiated by starving cells is severely impaired by the lack of myosin. The cells are unable to form multicellular aggregates normally and do not undergo subsequent morphogenesis. By changing the food source from liquid medium to bacteria, expression of the endogenous mhcA messenger RNA can be increased relative to expression of antisense RNA. When grown in this way, the transformed cells accumulate MHC A protein, remain mononucleate, and proceed through development normally.

Cell Movement↗
PubMed2003

Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA.

Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison revealed in 45 antisense RNA control systems a 5' YUNR motif indicative for the formation of a U-turn structure in either an antisense or a target RNA loop and confirmed in the case of the hok/sok system of plasmid R1 its importance for regulation.Here, we demonstrate the importance of the 5' YUNR motif in the target RNA (RNAII) loop L1 of the replication control system of plasmid pIP501. The effect of four individual mutations in L1 was studied in vivo and in vitro. Mutations that maintained the putative U-turn or swapped it from sense to antisense RNA were silent, whereas mutations that eliminated the 5'-YUNR motif showed two- to threefold elevated copy numbers in vivo in correlation with three- to fourfold reduced inhibition rate constants of the complementary RNAIII species in vitro, whereas the half-lives of all RNAIII species were not affected. ENU probing experiments confirmed the U-turn structure for the silent mutation (N-C) and disruption of this structure upon alteration of the invariant U or inversion of the YUNR motif-containing loop. RNA secondary structure probing excluded loop size alterations as a reason for altered inhibition rates. Implications for the pathway and efficiency of RNAII/RNAIII interaction, and hence, pIP501 copy-number control, are discussed.

Bacillus subtilis↗
PubMed2005

RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum.

The recent identification of antisense RNA in the transcriptomes of many eukaryotes has generated enormous interest. The presence of antisense RNA in Plasmodium falciparum, the causative agent of severe malaria, remains controversial. Elucidation of the mechanism of antisense RNA in P. falciparum synthesis is critical in order to demonstrate the origin and function of these transcripts. Therefore, a systematic analysis of antisense and sense RNA synthesis was performed using direct labeling experiments. Nuclear run on experiments with single-stranded DNA probes demonstrated that antisense RNA is synthesized in the nucleus at several genomic loci. Antisense RNA synthesis is sensitive to the potent RNA polymerase II inhibitor alpha-amanitin. Antisense and sense transcription was also detected in nuclei isolated from synchronized parasites, suggesting concurrent synthesis. In summary, our experiments directly demonstrate that antisense RNA synthesis is a common transcriptional phenomenon in P. falciparum, and is catalyzed by RNA polymerase II.

Animals↗
PubMed2000

Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA.

The antisense RNA, CopA, regulates the replication frequency of plasmid R1 through inhibition of RepA translation by rapid and specific binding to its target RNA (CopT). The stable CopA-CopT complex is characterized by a four-way junction structure and a side-by-side alignment of two long intramolecular helices. The significance of this structure for binding in vitro and control in vivo was tested by mutations in both CopA and CopT. High rates of stable complex formation in vitro and efficient inhibition in vivo required initial loop-loop complexes to be rapidly converted to extended interactions. These interactions involve asymmetric helix progression and melting of the upper stems of both RNAs to promote the formation of two intermolecular helices. Data presented here delineate the boundaries of these helices and emphasize the need for unimpeded helix propagation. This process is directional, i.e. one of the two intermolecular helices (B) must form first to allow formation of the other (B'). A binding pathway, characterized by a hierarchy of intermediates leading to an irreversible and inhibitory RNA-RNA complex, is proposed.

Bacterial Proteins↗
PubMed1991

Use of electrophoretic mobility to determine the secondary structure of a small antisense RNA.

Natural antisense RNAs have stem-loop (hairpin) secondary structures that are important for their function. The sar antisense RNA of phage P22 is unusual: the 3' half of the molecule forms an extensive stem-loop, but potential structures for the 5' half are not predicted to be thermodynamically stable. We devised a novel method to determine the secondary structure of sar RNA by examining the electrophoretic mobility on non-denaturing gels of numerous sar mutants. The results show that the wild-type RNA forms a 5' stem-loop that enhances electrophoretic mobility. All mutations that disrupt the stem of this hairpin decrease mobility of the RNA. In contrast, mutations that change the sequence of the stem without disrupting it (e.g. change G.U to A.U) do not affect mobility. Nearly all mutations in single-stranded regions of the structure also have no effect on mobility. Confirmation of the proposed 5' stem-loop was obtained by constructing and analyzing compensatory double mutants. Combinations of mutations that restore a base-pair of the stem also restore mobility. The genetic phenotypes of sar mutants confirm that the proposed secondary structure is correct and is essential for optimal activity of the antisense RNA in vivo.

Base Sequence↗
PubMed1997

Induction of Galphaq-specific antisense RNA in vivo causes increased body mass and hyperadiposity.

Transgenic BDF-1 mice harboring an inducible, tissue-specific transgene for RNA antisense to Galphaq provide a model in which to study a loss-of-function mutant of Galphaq in vivo. Galphaq deficiency induced in liver and white adipose tissue at birth produced increased body mass and hyperadiposity within 5 weeks of birth that persisted throughout adult life. Galphaq-deficient adipocytes display reduced lipolytic responses, shown to reflect a newly discovered, alpha1-adrenergic regulation of lipolysis. This alpha1-adrenergic response via phosphoinositide hydrolysis and activation of protein kinase C is lacking in the Galphaq loss-of-function mutants in vivo and provides a basis for the increased fat accumulation.

Adipose Tissue↗
PubMed1999

Inhibition of oncogene expression using vector-generated RNA antisense.

Antisense RNA expression vectors have been developed relatively recently as a means to study the role of specific oncogenes in malignant transformation. In this paper, strategies for the construction of antisense plasmid vectors from commercially available reagents are described. Techniques for the introduction of these vectors into cell lines and tumors are also described and preferred methods for the evaluation of biological effects are presented. Lastly, using specific examples, the limitations and potential artifacts associated with antisense vector use in the study of tumorigenesis are discussed.

Cloning, Molecular↗