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At least 289 records · Page 16Linked to original sources
PubMed2003

RNAi reveals anti-apoptotic and transcriptionally repressive activities of DAXX.

The function of DAXX, a highly conserved mammalian gene, has remained controversial; this is due, in part, to its identification in a variety of yeast two-hybrid screens. Targeted deletion in the mouse revealed that DAXX is essential for embryonic development. Furthermore, the increased levels of apoptosis observed in Daxx-knockout embryos and embryonic stem cell lines suggested that DAXX functions in an anti-apoptotic capacity. In contrast, overexpression studies showed that DAXX may promote apoptosis. Additional studies showed that, when overexpressed, DAXX could function as a transcriptional repressor. To clarify these matters, we have used RNAi to deplete endogenous DAXX and thereby assess DAXX function in cell lines previously tested in overexpression studies. Increased apoptosis was observed in DAXX-depleted cells, showing DAXX to be anti-apoptotic. The apoptosis induced by the absence of DAXX was rescued by Bcl-2 overexpression. In addition, transcriptional derepression was observed in RNAi-treated cells, indicating the ability of endogenous DAXX to repress gene expression and allowing for the identification of novel targets of DAXX repression, including nuclear factor kappaB (NF-kappaB)- and E2F1- regulated targets. Thus, depletion of DAXX by RNAi has verified the crucial role of endogenous DAXX as an anti-apoptotic regulator, and has allowed the identification of probable physiological targets of DAXX transcriptional repression.

Adaptor Proteins, Signal Transducing↗
PubMed2003

RNAi: mammalian oocytes do it without RNA-dependent RNA polymerase.

Studies in mutant organisms deficient in RNA interference (RNAi) and related post-transcriptional gene silencing implicated a role for a single class of RNA-dependent RNA polymerases (RdRp). Nevertheless, sequence homologs to these RdRps have not been found in coelomate organisms such as Drosophila or mammals. This lack of homologous sequences does not exclude that an RdRp functions in RNAi in these organisms because an RdRp could be acquired by horizontal transfer from an RNA virus. In fact, such a sequence is found in mice (Aquarius) and we observe that it is expressed in mouse oocytes and early embryos, which exhibit RNAi. We report here that cordycepin, an inhibitor of RNA synthesis, does not prevent Mos double-strand RNA (dsRNA) to target endogenous Mos mRNA in mouse oocytes and that targeting a chimeric Mos-EGFP mRNA with dsRNA to EGFP does not reduce the endogenous Mos mRNA, but does target the chimeric mRNA. These results indicate that an RdRp is not involved in dsRNA-mediated mRNA degradation in mammalian oocytes, and possibly in mammals in general, and therefore that only homologous sequences to the dsRNA are targeted for degradation.

Animals↗
PubMed2006

Rapid construction of Drosophila RNAi transgenes using pRISE, a P-element-mediated transformation vector exploiting an in vitro recombination system.

RNAi is a gene-silencing phenomenon mediated by double-stranded RNA (dsRNA) and has become a powerful tool to elucidate gene function. To accomplish rapid construction of transgenes expressing dsRNA in Drosophila, we developed a novel transformation vector, pRISE, which contains an inverted repeat of the attR1-ccdB-attR2 cassette for in vitro recombination and a pentameric GAL4 binding site for conditional expression. These features enabled us to construct RNAi transgenes without a complicated cloning scheme. In cultured cells and transgenic flies, pRISE constructs carrying dsRNA transgenes induced effective RNAi against an EGFP transgene and the endogenous white gene, respectively. These results indicate that pRISE is a convenient transformation vector for studies of multiple Drosophila genes for which functional information is lacking.

ATP-Binding Cassette Transporters↗
PubMed2004

RNAi in living mice.

By introducing double-stranded RNAs (dsRNAs), it was shown that mRNAs that share sequences are destroyed, and that the translation step is severely downregulated (RNAi). This technique was demonstrated to be a very powerful tool for reverse genetics in Caenorhabditis elegans. However, studies have shown that RNAi can be achieved in living mice. In this chapter, we used "green mice" and "green rats" as model animals to demonstrate silencing of green fluorescent protein (GFP) expression by RNAi. In order to silence the gene, we produced transgenic mouse lines that produce dsRNA that is driven by the H1 promoter. It was demonstrated that the transgenically expressed, double stranded RNA could silence the GFP throughout the body of the mouse or rat and throughout the lifetime.

Animals↗
PubMed2005

Modulation of gene expression by RNAi.

RNA interference (RNAi) is a form of posttranscriptional gene silencing in which the presence within the cell of double-stranded RNA (dsRNA) leads to the specific degradation of mRNA with a complimentary sequence. RNAi is a natural phenomenon that can be exploited as a powerful tool to study gene function by generating gene "knockdowns" in various cell types. RNAi is mediated by short interfering RNAs (siRNAs), which are generated within cells from long dsRNAs. To avoid generalized toxic effects, mammalian cells are transfected directly with 21-23-bp-long siRNAs generated either by chemical synthesis or obtained by a series of enzymatic reactions. The present chapter deals with siRNA design, synthesis, transfection, and readout of efficiency in a mammalian cell culture system. The general principle is illustrated by the functional knockdown of p97/VCP (valosin-containing protein) in HeLa cells using five different siRNA sequences.

Animals↗
PubMed2003

RNAi technology and its use in studying the function of nuclear receptors and coregulators.

Until just a few years ago, RNA interference (RNAi) technology was restricted to the research fields of plants, C. elegans or Drosophila. The discovery of gene silencing by in vitro synthesized double-stranded RNA (dsRNA) in mammalian cells has made the use of RNAi possible in nearly the entire life science kingdom. DNA vectors delivering small interfering RNA (siRNA) directed by polymerase III or polymerase II promoters to persistently inhibit target genes expression have extended this technology to study in vivo function of these genes. Recently, RNAi has been used as a powerful tool in the functional analysis of nuclear receptors and their coregulators. This short review will cover studies in this area.

Journal Article↗
PubMed2006

Toward silencing the burden of malaria: progress and prospects for RNAi-based approaches.

The discovery of RNA interference (RNAi) is one of the most significant of recent years, with potential for application beyond the laboratory to the clinic. As a tool for functional genomics, RNAi has permitted the characterization of genes in organisms that had previously remained recalcitrant to targeted gene manipulation. Efforts to understand its mode of action have revealed a central role in gene regulation and host defense. Finally, as a therapeutic tool, it has shown enormous promise in the control of a large array of diseases. Here we examine how RNAi is revolutionizing malaria research in an organism, the Anopheles mosquito, that until recently was essentially resistant to genetic study, and show how its application in both the mosquito vector and the Plasmodium parasite might ultimately lead to new ways of controlling and perhaps even eradicating this devastating disease.

Animals↗
PubMed2005

Mammalian RNAi: a practical guide.

Silencing of gene expression by RNA interference (RNAi) has become a powerful tool for the functional annotation of the Caenorhabditis elegans and Drosophila melanogaster genomes. Recent advances in the design and delivery of targeting molecules now permit efficient and highly specific gene silencing in mammalian systems as well. RNAi offers a simple, fast, and cost-effective alternative to existing gene targeting technologies both in cell-based and in vivo settings. Synthetic small interfering RNA (siRNA) and retroviral short hairpin RNA (shRNA) libraries targeting thousands of human and mouse genes are publicly available for high-throughput genetic screens, and knockdown animals can be rapidly generated by lentivirus-mediated transgenesis. RNAi also holds great promise as a novel therapeutic approach. This review provides insight into the current gene silencing techniques in mammalian systems.

Animals↗
PubMed2004

Recent applications of RNAi in mammalian systems.

RNAi is a powerful cellular mechanism that involves targeted destruction of mRNAs. Although the phenomenon was first discovered in plants and lower eukaryotic organisms, it was later discovered as an important genetic regulatory mechanism in mammalian cells. RNAi is triggered by double stranded RNAs that are cleaved into short 21-23 base pair duplexes by an RNAse III type enzyme called Dicer. The short RNAs, termed small interfering RNAs (siRNAs), act as triggers for targeted RNA degradation. One of the two strands is selectively incorporated into a complex of proteins called the RNA induced silencing complex, or RISC. The incorporated small RNA guides the complex to the complementary target sequence, and this event is followed by endonucleolytic cleavage of the target and recycling of RISC. In mammalian cells, siRNAs do not activate interferon pathway genes, thereby making these powerful tools for sequence specific knockdown of RNAs. In this article we review the methods for programming mammalian cells with siRNAs, and overview a number of applications ranging from targeting oncogenes to inhibiting viral replication. The article also summarizes some important biological conclusions that can be drawn from selective downregulation of certain mRNA targets and addresses potential uses of RNAi as a new therapeutic modality.

Animals↗
PubMed2001

Rnai: a new technology in the post-genomic sequencing era.

The complete genome sequences and huge numbers of predicted gene sequences from many complex organisms are available. Reverse-genetic analyses of these organisms will now be necessary to understand what all these genes are doing and how their functions interact. RNAi technology is very useful in this regard for studying gene function, not only in these model organisms, but also in the organisms previously considered not to be amenable to genetic analysis. This treatment reviews the discovery of RNAi, advances in the study of the mechanisms by which this material impinges on gene-product expressions, and technical improvements that will allow RNAi to be applied to a wide variety of organisms.

Animals↗
PubMed2005

[Inhibition of HBV core antigen gene expression in human embryonic kidney cell line AD293 by plasmid-based RNAi].

OBJECTIVE: To inhibit HBV core antigen gene expression with plasmid-based RNAi. METHODS: The shRNA expression vector targeting HBV core antigen gene was designed and constructed. Human embryonic kidney cell line AD293 was co-transfected with HBcAg-EGFP fusion protein expression vector and shRNA expression vector transiently, and the cells without shRNA-transfection and with non-specific shRNA transfection were used as controls. Inhibitory effect of RNAi was detected by fluorescence-activated cell sorting (FACS) and real-time fluorescence quantificational RT-PCR. RESULTS: HBV core antigen gene expression in AD293 was inhibited by shRNA, with the maximal inhibition rate of 76 % measured by FACS and of 63.1 % by real-time PCR. CONCLUSION: Effective inhibition of HBV core antigen gene expression by plasmid-based RNAi provides an alternative for anti-HBV study in vitro, which has potential clinical application.

Cell Line↗
PubMed2005

[Application of RNAi in gene-deficient models].

RNA interference (RNAi), a process of sequence-specific gene silence,can effectively and specifically suppress the activity of corresponding mRNAs in a gene-dependent manner induced by double-stranded RNA (dsRNA). This powerful technology has been widely employed to manipulate gene expression in mammalian and human cells, elucidate signal transduction pathways and identify gene functions in a whole-genome scale. Simultaneously, it also displays a bright and fascinating future in the research and development of RNAi-based drugs for various diseases such as viral infections, cancers, metabolic disorders and genetic diseases. In present review, we attempt to recapitulate the application of this breakthrough technology in establishing gene-deficient models and show the alluring foreground of RNAi-based gene therapy in these diseases.

Animals↗
PubMed2005

RNAi and high-content screening in target identification and validation.

The development of effective novel therapeutic agents faces many significant challenges, such as demonstrating that a candidate target plays a critical role in disease progression. RNA interference (RNAi) has proven to be a robust and highly scalable technology, and as such, has become an essential method for studying targets in many disease models. High-content screening (HCS) is a platform for quantitatively measuring cellular features such as transcription factor localization. This is a more powerful method of measuring signal transduction than reporter assays because the image-based data of HCS can eliminate many sources of assay artifacts, and the associated statistical tools are highly effective. While it appears obvious that convergence of technologies is required to establish RNAi screening assays in HCS formats, some challenges arise when combining the approaches. However, combining RNAi and HCS provides significant and unique advantages to a target validation program.

Animals↗
PubMed2006

Using RNAi in the clinic.

RNA interference (RNAi) is a biological process that controls gene silencing in all living cells. Targeting the RNAi system represents a novel therapeutic strategy that has the ability to intercede with multiple disease-related genes and so target many human diseases. Recently, the design of small interfering RNA (siRNA)-selective compounds has become more straightforward because of the significant progress made in predictive modeling. Exciting new data show that siRNA blocks gene function in vivo, suggesting that it has potential as a therapeutic approach for humans. This article highlights recent advances in siRNA research and discusses the aims of the pharmaceutical and biotechnology industries to progress siRNA compounds into the clinical. In the fight against disease, the use of RNAi is a powerful new tactic that adds to the arsenal of small-molecule inhibitors and antibody-blocking approaches.

Animals↗
PubMed2006

[Reversion of multidrug resistance (MDR) in human glioma cells by RNA interference (RNAi)].

OBJECTIVE: To explore whether the constructed vector of short haprin in vivo can induce human glioma cell line BT325 to produce RNAi duplexes and reverse the expression of MDR1 gene. METHODS: Three 62nt oligonucleotide fragments (shRNA) were constructed according to GenBank MDR1 sequence and were cloned to the retrovirus-delivered vectors. After transfected these vectors directly into the human malignant glioma BT325 cells by lipofectamine 2000 with enhanced green fluorescence protein (EGFP) co-transfecting, the MDR1 gene silence effects were detected by the changing level of mRNA and P-glycoprotein including real time PCR (RT-PCR), Northern blot and Western blot analysis. To assess the multidrug resistance against adriamycin (ADR) and VCR, cell proliferation assays were performed by cell counting kit-8. RESULTS: The RNAi plasmid vectors were constructed successfully. RT-PCR showed MDR1 mRNA was significantly reduced (P < 0.05). Northern blot analysis showed that the gene silence became most intense at 48 hours after transfection. Western blot analysis demonstrated that P-gp expression was reduced at different time to 12.9%, 30.3% and 4.8%, respectively. The chemosensitivity assays indicated that the transfected cells showed an enhanced sensitivity to ADR and VCR. Based on the value of IC(50), BT325 cells had significantly increased sensitivity to the drugs. CONCLUSION: The sequence specific RNAi can inhibit MDR1 mRNA and P-gp expression in the glioma cell line. It may reverse multidrug resistance phenotype, therefore, may provide promising therapeutic modalities in the treatment of human glioma.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2026

Systematic identification of germ granule proteins reveals specialized roles in RNAi and small RNA inheritance.

Biomolecular condensates, such as germ granules, organize RNAi pathways critical for fertility and genome regulation. However, the protein composition and functional contributions of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that contribute to fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors associated with defects in WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has coevolved with PRG-1 across clade V nematodes, with a conserved structured N terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily coadapted PIWI interactor critical for siRNA biogenesis.

Animals↗
PubMed2005

New tool for an old problem: can RNAi efficiently resolve the issue of genetic redundancy?

RNA interference (RNAi) has become a generally accepted tool for inhibiting gene expression in many laboratory organisms. Nagel et al.,(1) in a recent paper, give an example of how this tool can also be used to address the question of genetic redundancy. Their focus was on the redundancy in Drosophila melanogaster of the Enhancer of split gene complex [E(spl)-C] which comprises seven highly related genes. Their somewhat conflicting findings are probably the typical scenario for most RNAi experiments: some expected results and some surprises.

Animals↗
PubMed2006

Application of lentivirus-mediated RNAi in studying gene function in mammalian tooth development.

RNA interference (RNAi) has recently become a powerful tool to silence gene expression in mammalian cells, but its application in assessing gene function in mammalian developing organs remains highly limited. Here we describe several unique developmental properties of the mouse molar germ. Embryonic molar mesenchyme, but not the incisor mesenchyme, once dissociated into single cell suspension and re-aggregated, retains its odontogenic potential, the capability of a tissue to instruct an adjacent tissue to initiate tooth formation. Dissociated molar mesenchymal cells, even after being plated in cell culture, retain odontogenic competence, the capability of a tissue to respond to odontogenic signals and to support tooth formation. Most interestingly, while dissociated epithelial and mesenchymal cells of molar tooth germ are mixed and re-aggregated, the epithelial cells are able to sort out from the mesenchymal cells and organize into a well-defined dental epithelial structure, leading to the formation of a well-differentiated tooth organ after sub-renal culture. These unique molar developmental properties allow us to develop a strategy using a lentivirus-mediated RNAi approach to silence gene expression in dental mesenchymal cells and assess gene function in tooth development. We show that knockdown of Msx1 or Dlx2 expression in the dental mesenchyme faithfully recapitulates the tooth phenotype of their targeted mutant mice. Silencing of Barx1 expression in the dental mesenchyme causes an arrest of tooth development at the bud stage, demonstrating a crucial role for Barx1 in tooth formation. Our studies have established a reliable and rapid assay that would permit large-scale analysis of gene function in mammalian tooth development.

Animals↗