Presence Of Antisense RNA Research Articles

Use of antisense RNA to modulate glycosyltransferase gene expression and exopolysaccharide molecular mass in Lactobacillus rhamnosus

Discovery of gene function requires inactivation in order to demonstrate the effect of the absence of gene expression on cell phenotype. As gene inactivation can be lethal, such mutations are often unattainable. Antisense RNA provides a method of reducing transcript and protein levels without totally inactivating the targeted gene, thus providing information on the gene's possible function. This study demonstrates the use of antisense RNA to modulate polysaccharide size in Lactobacillus rhamnosus, a bacterial species with technological and health applications in fermented milk products. Production of antisense RNA coding for a glycosyltransferase leads to reduced sense RNA transcript. While the total amount of polysaccharide produced was not significantly affected, size exclusion chromatography showed that polysaccharides of different molecular mass were produced in the presence of antisense RNA. Conditional control over gene expression could thus be useful for metabolic engineering strategies, where gene inactivation is not practicable.

An improved RNA amplification procedure results in increased yield of autologous RNA transfected dendritic cell-based vaccine

Use of antigen encoding RNA transfected Dendritic cells in the field of cancer immunotherapy has been well established. The use of RNA overcomes limitations inherent to other autologous DC-based vaccines as it does not require specific HLA haplotypes, identification and characterization of antigens, and captures the broadest antigen repertoire. RNA offers yet another advantage-it could be amplified minimizing the requirement of tumor mass for autologous vaccine production, and will afford the opportunity to treat patients with minimal tumor burden. The original procedure described for RNA amplification resulted in a proportion of RNA transcribed in the antisense orientation. This study also demonstrates that the presence of double-stranded RNA correlates with the presence of antisense RNA. Alternative design of oligonucleotides that removes sequence redundancy eliminates the formation of both antisense and double-stranded RNA species. We provide further evidence that amplified RNA containing antisense and double-stranded RNA species results in lower recovery of DCs post-transfection and maturation, presumably through sequence-specific gene silencing. The removal of the double-stranded species from amplified RNA results in higher recovery of mature autologous amplified RNA transfected dendritic cells. Higher DC yield will allow for reduction of cost of vaccine manufacturing and prolonged treatment of a patient.

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.

Post‐transcriptional Silencing of the Tomatinase Gene in Fusarium oxysporum f. sp lycopersici

Abstract Fusarium oxysporum f. sp. lycopersici produces an extracellular enzyme tomatinase, which has been known to detoxify α‐tomatine, a preformed inhibitor of fungal growth in tomato plants. To understand the role of the tomatinase in pathogenicity, we performed transformation‐mediated disruption of the tomatinase gene in F. oxysporum f. sp. lycopersici. Mutants obtained showed increase in sensitivity to α‐tomatine and decrease in tomatinase activity in vitro. Inoculation assay showed reduced pathogenicity of the mutants on tomato plants, suggesting an important role of tomatinase in pathogenicity of this fungus. However, Southern blot analysis revealed that the resident tomatinase gene of the mutants was not disrupted but the gene replacement vector was ectopically integrated into the genome of the mutants. To clarify the mechanisms involved, we examined one of the ectopic insertion mutants at both DNA and RNA levels. No methylation of the resident tomatinase gene was detected. Northern blot analysis revealed low level of the tomatinase gene expression and also the presence of antisense RNA in the ectopic mutant. Thus, post‐transcriptional gene silencing seems to be involved in the suppression of tomatinase in the ectopic mutant.

Regulation of the NPT gene by a naturally occurring antisense transcript.

The epithelial Na/Pi cotransporter (NaPi-II) is instrumental in maintaining phosphate (Pi) homeostasis in vertebrates. Hormones and metabolic factors (PTH, Pi availability) that acutely influence renal Pi excretion have been demonstrated to target NaPi-II expression. Upon stimulation, newly synthesized transporter molecules become integrated into the brush-border membrane to increase the Vmax of Pi uptake; reduction of Pi reabsorption is achieved by endocytosis of NaPi-II followed by lysosomal degradation of the protein. The long-term regulation of the protein is less well studied. Only recently, regulatory elements for vitamin D3 and Pi have been identified in the promoter region of the npt gene. However, signaling pathways leading to the activation of these regulatory sequences need to be established. Other reports suggested messenger RNA stability to play a role in the medium range regulation of NaPi-II expression. Recent findings in our laboratory added to the complex picture of npt gene regulation. We have identified npt-related endogenous antisense transcripts from mouse, zebrafish, and winter flounder. The two fish transcripts have been cloned and characterized; the mouse homolog has only very recently been detected. The transcripts are devoid of an open reading frame and appear in different splice forms. The evolutionary conservation of bidirectional transcription of the npt gene implies a regulatory function for the antisense transcript. In order to test the functional consequences of bidirectional transcription, we coexpressed sense and the antisense transcripts from zebrafish in Xenopus oocytes. Pi transport activity was reduced as a result of the presence of antisense RNA. Re-extraction of the RNA from injected oocytes followed by Northern blot revealed that the coexpression had no significant effect on the stability of either transcript. We concluded that the antisense mRNA interfered with the translation of the transporter if coexpressed in the Xenopus system. However, the regulatory mechanism(s) involving the npt-related antisense transcript is expected to be much more complicated in vivo, (i.e., requiring supplementary factors like double-stranded RNA recognizing proteins or specific RNases). It is planned to test this hypothesis by a transgenic zebrafish approach and/or knockout mice.

Co-suppression of the hydrophobin gene HCf-1 is correlated with antisense RNA biosynthesis in Cladosporium fulvum.

Transformation of Cladosporium fulvum with DNA containing a truncated copy of the hydrophobin gene HCf-1 causes co-suppression of hydrophobin synthesis in 30% of the transformants. The co-suppressed isolates have a hydrophilic phenotype, lower levels of HCf-1 mRNA than wild type and contain multiple copies of the plasmid integrated as tandem repeats at ectopic sites in the genome. Gene silencing is not associated with DNA cytosine methylation. Nuclear run-off experiments reveal that transcription rate of HCf-1 in the co-suppressed isolates is higher than in the untransformed strains, suggesting that silencing acts at the post-transcriptional level. We show, for the first time in fungi, that co-suppression is correlated with the presence of antisense RNA, and that this is synthesised on a DNA template. Derivatives showing reversion to the wild-type phenotype and restoration of HCf-1 gene expression were also observed. Reversion is associated with loss of some copies of the transgene. We propose that co-suppression is due to ectopic integration of the transgene next to promoters which initiate transcription to form antisense RNA and that this in turn determines down-regulation of HCf-1.

Completion of Avian Retroviral DNA Replication Intermediates Inhibited by Antisense RNA

High level expression of RNA complementary to either neo r or src sequences located near the 3′ end of recombinant retroviral vectors derived from Rous sarcoma virus inhibited viral replication. Stable integration of proviral DNA was not detected in the presence of antisense RNA. We investigated the mechanism of this inhibition by determining the structure of unintegrated viral DNA (vDNA) intermediates accumulating in the presence of the anti-sense RNA. The major vDNA intermediate detected was a full-length duplex linear molecule with complementary single-stranded long terminal repeats (LTRs). These vDNA linears could be joined directly by T4 DNA ligase to form junctions which contained a single normal LTR, These results can be explained by arrest of linear vDNA formation before strand displacement results in completion of the LTRs. Isolation of these sticky-ended intermediates as linear rather than nicked circular molecules suggests that these complementary vDNA LTR segments were not hydrogen bonded in the infected cell and further implies that completion of LTR synthesis is an ordered, controlled process.

Presence and distribution of human papillomavirus sense and antisense RNA transcripts in genital cancers

RNA transcription in eight human papillomavirus (HPV) type 16-positive genital carcinomas and in two cervical squamous cell carcinoma (SCC)-derived cell lines was analysed by in situ hybridization using 125I-labelled subgenomic riboprobes. Transcripts corresponding to the E6 and E7 open reading frames were always present, except within the keratinizing layers of differentiated SCCs. Intranuclear E1 gene transcripts were detectable in both cell lines and some tumours whereas E2/E4 transcripts were absent from five of seven assessable tumours, suggesting transcription from integrated viral DNA. When mRNA sense riboprobes were used as controls, no signal was seen in the two cell lines; however, three tumours contained a focal, intense nuclear RNase-sensitive signal using mRNA sense riboprobes. This antisense RNA signal mapped across the whole genome including the noncoding region. In one tumour, the presence of antisense RNA was independently confirmed by using E7 and E2/E4 RNA probes of both orientations in RNase protection assays. Transcription of antisense RNA may be a natural feature of some HPV-positive genital tumours and its possible role in modulating cell behaviour in vivo requires further investigation.

The influence of antisense RNA on transcriptional mapping of the 5' terminus of a baculovirus RNA

S1 nuclease protection and primer extension analyses were used to determine the 5' end of the Autographa californica nuclear polyhedrosis virus 603 open reading frame (ORF) transcript upstream of and on the opposite strand to the polyhedrin gene. These analyses suggested that the 5' end of the 603 ORF was located near the initiation site for polyhedrin gene transcription. Primer extension products of reverse transcription of 603 RNA were dependent on the presence of the TAAG sequence, an essential polyhedrin promoter element. The results could be interpreted as indicating bidirectional transcription from the TAAG element. However, the data could also be due to an artefact of antisense transcripts and RNA duplex formation in this region. Since the bidirectional transcriptional model is not consistent with other mapping data and Northern blot analysis, we conclude that the presence of antisense RNA can result in mapping artefacts and that caution must be taken in interpreting data where overlapping sense and antisense RNAs are present.

The conditional inhibition of gene expression in culturedDrosophilacells by antisense RNA

Genes producing antisense RNA are becoming important tools for the selective inhibition of gene expression. Experiments in different biological systems, targeting different mRNAs have yielded diverse results with respect to the success of the technique and its mechanism of action. We have examined the potential of three antisense genes, whose transcription is driven by a Drosophila metallothionein promoter, to inhibit the expression of alcohol dehydrogenase (ADH) or a microtubule associated protein (205K MAP) in cultured Drosophila cells. Expression of ADH was significantly reduced upon induction of the anti-ADH genes. The ADH mRNA does not appear to be destabilized by the presence of antisense RNA but rather exists at similar levels in hybrid form. Hybrids are detected with both spliced and unspliced ADH RNA. In contrast to these results, antisense genes producing antisense RNA in great excess to 205K MAP mRNA, which is itself far less abundant than the ADH mRNA, failed to show any inhibition of 205K MAP expression.