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At least 541 records · Page 30Linked to original sources
PubMed2004

[Reversal of multi-drug resistance in K562/A02 cells by small interference RNA of mdr1 gene].

OBJECTIVE: To investigate the effect of small interference RNA (siRNA) on mdr1 and P-glyco-protein (P-gp) expression of multi-drug resistance (MDR) human leukemia cell line K562/A02. METHODS: Three si RNAs (si-mdr1-1, si-mdr1-2, si-mdr1-3) which were specifically targeted mdr1 gene were synthesized and transfected into K562/A02 cells. Expression of mdr1 mRNA was assayed by RT-PCR. P-gp expression and intracellular daunorubicin (DNR) concentration were determined by flow cytometry. 50% inhibition concentration (IC(50)) of doxorubicin (ADM) on K562/A02 was determined by MTT method. RESULTS: Treatment of K562/A02 cell with the 3 kinds of siRNAs resulted in a reversal of MDR of a different extent. The third siRNA was more effective in the suppression of mdr1 with a significant reduction of (58.0 +/- 1.54)% of the mdr1 mRNA expression. Positive expression rate of p170 decreased from (76.0 +/- 1.0)% to (19.6 +/- 1.9)%, and the relative efficiency of K562/A02 to ADM was 70.4%. The intracellular accumulation of DNR increased after siRNA treatment. CONCLUSION: The siRNA could effectively restore the sensitivity of K562/A02 cells to conventional chemotherapeutic agents.

Base Sequence↗
PubMed2006

[Apoptosis of glioma cell line U251 induced by small interfering RNA targeting survivin].

OBJECTIVE: To construct recombinant expression vectors of small interfering RNA (siRNA) targeting survivin and investigate apoptosis of glioma cell line U251 mediated by the survivin-targeting siRNA. METHODS: According to the sequence of the coding region of survivin gene, two strings of 19 nucleotides of inverted sequence flanking the loop sequence of two complementary 9-base oligonucleotides were designed and synthesized to form hairpin construct as the DNA templates for the target siRNA. The siRNA templates were cloned into siRNA expression vector pGenesil-1, and the resulted vector pGenesil-1/survivin was transfected into U251 cells using Metafectene following the standard protocols. Real-time PCR and Western blotting were performed to evaluate survivin gene silencing induced by siRNA transfection at the RNA and protein levels, respectively. Flow cytometry analysis with Annexin-V/PI double staining was used to determine the cell apoptosis. RESULTS: Real-time RT-PCR and Western blotting revealed significantly lowered survivin expression at both RNA and protein levels in transfected U251 cells, which exhibited a significantly higher apoptosis rate after transfection as shown by flow cytometry analysis. CONCLUSION: RNA interference mediated by the siRNA expression vector pGenesi-l/survivin can significantly reduce survivin expression and induce remarkable apoptosis in U251 cells.

Apoptosis↗
PubMed1998

Inhibitors of protein-RNA complexation that target the RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules.

TAR RNA represents an attractive target for the intervention of human immunodeficiency virus type 1 (HIV-1) replication by small molecules. We now describe three small molecule inhibitors of the HIV-1 Tat-TAR interaction that target the RNA, not the protein. The chemical structures and RNA binding characteristics of these inhibitors are unique for each molecule. Results from various biochemical and spectroscopic methods reveal that each of the three Tat-TAR inhibitors recognizes a different structural feature at the bulge, lower stem, or loop region of TAR. Furthermore, one of these Tat-TAR inhibitors has been demonstrated, in cellular environments, to inhibit (a) a TAR-dependent, Tat-activated transcription and (b) the replication of HIV-1 in a latently infectious model.

Allosteric Regulation↗
PubMed1990

Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing.

U6 is one of the five small nuclear RNA's (snRNA's) that are required for splicing of nuclear precursor messenger RNA (pre-mRNA). The size and sequence of U6 RNA are conserved among organisms as diverse as yeast and man, and so it has been proposed that U6 RNA functions as a catalytic element in splicing. A procedure for in vitro reconstitution of functional yeast U6 small nuclear ribonucleoproteins (snRNP's) with synthetic U6 RNA was applied in an attempt to elucidate the function of yeast U6 RNA. Two domains in U6 RNA were identified, each of which is required for in vitro splicing. Single nucleotide substitutions in these two domains block splicing either at the first or the second step. Invariably, U6 RNA mutants that block the first step of splicing do not enter the spliceosome. On the other hand, those that block the second step of splicing form a spliceosome but block cleavage at the 3' splice site of the intron. In both domains, the positions of base changes that block the second step of splicing correspond exactly to the site of insertion of pre-mRNA-type introns into the U6 gene of two yeast species, providing a possible explanation for the mechanism of how these introns originated and adding further evidence for the proposed catalytic role of U6 RNA.

Base Sequence↗
PubMed2000

The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance.

During the early stages of transcription, T7 RNA polymerase forms an unstable initiation complex that synthesizes and releases transcripts 2-8 nt in length before disengaging from the promoter and isomerizing to a stable elongation complex. In this study, we used RNA small middle dotprotein and RNA small middle dotDNA crosslinking methods to probe the location of newly synthesized RNA in halted elongation complexes. The results indicate that the RNA in an elongation complex remains in an RNA small middle dotDNA hybrid for about 8 nt from the site of nucleotide addition and emerges to the surface of the enzyme about 12 nt from the addition site. Strikingly, as the transcript leaves its hybrid with the template, the crosslinks it forms with the RNA polymerase involve a portion of a hairpin loop (the specificity loop) that makes specific contacts with the binding region of the promoter during initiation. This observation suggests that the specificity loop may have a dual role in transcription, binding first to the promoter and subsequently interacting with the RNA product. It seems likely that association of the nascent RNA with the specificity loop facilitates disengagement from the promoter and is an important part of the process that leads to a stable elongation complex.

Bacteriophage T7↗
PubMed2006

Use of herpes simplex virus type 1-based amplicon vector for delivery of small interfering RNA.

Silencing of gene expression by small interfering RNAs (siRNAs) is rapidly becoming a powerful tool for genetic analysis of mammalian cells. The use of DNA-based plasmid vectors to achieve transient and stable expression of siRNA has been developed to avoid the problems of double-stranded oligonucleotides transfection. These vectors direct the transcription of small hairpin RNAs (shRNAs) from a polymerase-III (H1 or U6)-RNA gene promoter. However, numerous disadvantages remain, including low transfection efficiency and difficulty in transfecting primary cells. To overcome some of these problems, the use of viral vectors for siRNA delivery has been described. Retroviral, adenoviral, adeno-associated and herpes viral shRNAs delivery systems have been successfully used to silence genes, in vitro and in vivo. The use of a herpes simplex virus type 1 (HSV-1)-based amplicon vector for siRNA delivery into mammalian cells, using human polyomavirus BK (BKV)-transformed cells as a model system is described. The results demonstrate the ability of amplicon vectors to inhibit the expression of BKV T-Ag and tumorigenicity of BKV-transformed cells. We show that the use of the amplicon vector is highly efficient for the delivery of siRNA molecules. The unique ability of these vectors to deliver multiple copies of siRNA may provide a useful tool in the development of novel anticancer therapy.

Animals↗
PubMed2003

Small interfering RNA (siRNA) targeting VEGF effectively inhibits ocular neovascularization in a mouse model.

PURPOSE: RNA interference mediated by small interfering RNAs (siRNAs) is a powerful technology allowing the silencing of mamalian genes with great specificity and potency. The purpose of this study was to demonstrate the feasibility of RNA interference mediated by siRNA in retinal cells in vitro and in the murine retina in vivo. METHODS: siRNAs specific for enhanced green fluorescent protein (EGFP) and murine and human vascular endothelial growth factor (VEGF) were designed. In vitro studies in human cell lines entailed modulation of endogenous VEGF levels through chemically induced hypoxia. Effects of siRNA treatment on these levels were measured by ELISA. In vivo studies evaluating effects of siRNA on levels of EGFP and VEGF were performed by co-injecting recombinant viruses carrying EGFP or hVEGF cDNAs along with the appropriate siRNAs subretinally in mice. Additional studies aimed at blocking production of endogenous mVEGF were performed using laser-induced choroidal neovascularization (CNV) in mice. Effects of in vivo treatments were evaluated ophthalmoscopically. Retinal/choroidal flat mounts were evaluated after perfusion with dextran-fluorescein. Alternatively, retinas were evaluated in histological sections or VEGF levels were measured in intact eyes using ELISA. RESULTS: Successful delivery of siRNA to the subretinal space was confirmed by observing significantly reduced levels of EGFP in eyes treated with Ad.CMV.EGFP plus EGFP-directed siRNA. siRNAs directed against hVEGF effectively and specifically inhibit hypoxia-induced VEGF levels in human cell lines and after adenoviral induced hVEGF transgene expression in vivo. In addition, subretinal delivery of siRNA directed against murine Vegf significantly inhibited CNV after laser photocoagulation. CONCLUSIONS: Delivery of siRNA can be used in vitro and in vivo to target specific RNAs and to reduce the levels of the specific protein product in the targeted cells. This work suggests that RNA interference has potential for application to studies of retinal biology and for the treatment of a variety of retinal diseases, including those involving abnormal blood vessel growth.

Adenoviruses, Human↗
PubMed1991

Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA.

Multiple processing events are required to convert a single eukaryotic pre-ribosomal RNA (pre-rRNA) into mature 18S (small subunit), 5.8S and 25-28S (large subunit) rRNAs. We have asked whether U3 small nucleolar RNA is required for pre-rRNA processing in vivo by depleting Saccharomyces cerevisiae of U3 by conditional repression of U3 synthesis. The resulting pattern of accumulation and depletion of specific pre-rRNAs indicates that U3 is required for multiple events leading to the maturation of 18S rRNA. These include an initial cleavage within the 5' external transcribed spacer, resembling the U3 dependent initial processing event of mammalian pre-rRNA. Formation of large subunit rRNAs is unaffected by U3 depletion. The similarity between the effects of U3 depletion and depletion of U14 small nucleolar RNA and the nucleolar protein fibrillarin (NOP1) suggests that these could be components of a single highly conserved processing complex.

Animals↗
PubMed1996

Identification of a SPH element in the distal region of a human U6 small nuclear RNA gene promoter and characterization of the SPH binding factor in HeLa cell extracts.

Vertebrate small nuclear RNA (snRNA) gene promoters contain a distal, enhancer-like region that is composed of an octamer motif adjacent to at least one other element. Here we show that a human U6 snRNA distal region contains a SPH motif previously found in several chicken snRNA gene enhancers and the 5'-flanking region of vertebrate selenocysteine tRNA genes. SPH binding factor (SBF) was detected in either chicken or HeLa cell extracts that could bind SPH elements in a species-independent manner. Both human and chicken SBF required divalent cation to bind effectively to DNA. DNase I footprinting experiments indicated that human SBF specifically protected the human U6 SPH element. Furthermore, a SBF polypeptide of approximately 85 kDa was detected in both HeLa and chicken extracts following ultraviolet light-mediated cross-linking to human U6 or chicken U4 SPH elements. A part of the human U6 SPH element was quite sensitive to mutation, as demonstrated by both specific protein binding and transcription assays. From these data it is apparent that the distal regions of some RNA polymerase III- and RNA polymerase II-transcribed small RNA promoters are virtually identical in composition, and their mechanisms of transcriptional activation are possibly quite similar.

Animals↗
PubMed1978

Rat liver nuclear skeleton and small molecular weight RNA species.

Small molecular weight RNA species (smwRNAs) were studied in rat liver nuclei with and without chromatin as well as with and without nuclear envelope and nucleoplasm. From all the species identified, only two, N5 and 5Sb, were related to ribosomes. The others were localized exclusively in the nuclear skeleton or the spongelike network that was described in the preceding communication. This network or protein matrix contains a less abundant but exclusive set of molecules designated 5Sa, N1, and 4.5S, as well as other more abundant molecules which also exist in rat liver endoplasmic reticulum but not in polysomes or postribosomal RNP complexes. The smwRNAs behave like HnRNA; they remain located in the nuclear skeleton when nuclei are deprived of nucleoplasm and chromatin. With the information presently available, it is not possible to know whetherer both species are in the same or different RNP complexes and whether some of the smwRNAs contribute to the architecture of the nuclear skeleton. Distinct from any other nuclear RNA species, smwRNAs have two unique properties: facility of extraction, and resistance to nuclear ribonuclease digestion.

Animals↗
PubMed1995

Depletion of small cytoplasmic RNA confers fusidic-acid resistance on Bacillus subtilis.

Bacillus subtilis small cytoplasmic RNA (scRNA) is a member of a signal recognition particle (SRP)-like RNA family. To analyze the function of scRNA in protein synthesis, a B. subtilis strain SC201NA was constructed in which the expression of intact scRNA is regulated by an IPTG-inducible promoter. In this strain, depletion of scRNA leads to deficient translation and sporulation as well as morphological changes. In addition, the growth of SC201NA in the absence of IPTG became fusidic-acid resistant. The acquisition of fusidic-acid resistant phenotype by depletion of scRNA suggested that scRNA is associated with elongation factor G (EF-G) in the translation process.

Bacillus subtilis↗
PubMed2006

Inducible and reversible suppression of Npm1 gene expression using stably integrated small interfering RNA vector in mouse embryonic stem cells.

The tetracycline (Tc)-inducible small interference RNA (siRNA) is a powerful tool for studying gene function in mammalian cells. However, the system is infrequently utilized in embryonic stem (ES) cells. Here, we present the first application of the Tc-inducible, stably integrated plasmid-based siRNA system in mouse ES cells to down-regulate expression of Npm1, an essential gene for embryonic development. The physiological role of Npm1 in ES cells has not been defined. Our data show that the knock-down of Npm1 expression by this siRNA system was not only highly efficient, but also Tc- dose- and induction time-dependent. Particularly, the down-regulation of Npm1 expression was reversible. Importantly, suppression of Npm1 expression in ES cells resulted in reduced cell proliferation. Taken together, this system allows for studying gene function in a highly controlled manner, otherwise difficult to achieve in ES cells. Moreover, our results demonstrate that Npm1 is essential for ES cell proliferation.

Animals↗
PubMed2002

Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5.

Double-stranded RNAs approximately 21 nucleotides long [small interfering RNA (siRNA)] are recognized as powerful reagents to reduce the expression of specific genes. To use them as reagents to protect cells against viral infection, effective methods for introducing siRNAs into primary cells are required. Here, we describe success in constructing a lentivirus-based vector to introduce siRNAs against the HIV-1 coreceptor, CCR5, into human peripheral blood T lymphocytes. With high-titer vector stocks, >40% of the peripheral blood T lymphocytes could be transduced, and the expression of a potent CCR5-siRNA resulted in up to 10-fold inhibition of CCR5 expression on the cell surface over a period of 2 weeks in the absence of selection. In contrast, the expression of another major HIV-1 coreceptor, CXCR4, was not affected. Importantly, blocking CCR5 expression by siRNAs provided a substantial protection for the lymphocyte populations from CCR5-tropic HIV-1 virus infection, dropping infected cells by 3- to 7-fold; only a minimal effect on infection by a CXCR4-tropic virus was observed. Thus, our studies demonstrate the feasibility and potential of lentiviral vector-mediated delivery of siRNAs as a general means of intracellular immunization for the treatment of HIV-1 and other viral diseases.

Acquired Immunodeficiency Syndrome↗
PubMed1987

Transcriptional signals of a U4 small nuclear RNA gene.

The signals controlling the expression of a chicken U4 small nuclear RNA (snRNA) gene have been studied by microinjection into Xenopus oocytes. At least two distinct regions in the 5'-flanking DNA contribute to U4B RNA gene expression. The proximal regulatory element, which is inactivated by a 5'-flanking DNA deletion to position -38, provides a basal level of U4B RNA synthesis. The distal regulatory region, centered near position -200, acts as a transcriptional enhancer. It provides a 4-5 fold stimulation of U4B RNA gene expression above the basal level, and, like mRNA enhancers, is composed of multiple functional motifs. One of these, the octamer sequence ATGCAAAG, has previously been recognized as an important element of U1 and U2 snRNA gene enhancers, as well as being involved in the expression of a number of mRNA genes. However, the octamer sequence is not sufficient for U4B enhancer activity. An additional element, an "Sph motif," is located 12 base pairs downstream of the octamer and is an essential component of the U4B enhancer. Transcriptional competition studies indicate that the U4B and U1 snRNA genes utilize a common set of transcription factors.

Animals↗
PubMed1997

Characterization of a Drosophila proximal-sequence-element-binding protein involved in transcription of small nuclear RNA genes.

In a wide variety of eukaryotic organisms, transcription of small nuclear RNA (snRNA) genes is dependent upon a proximal sequence element (PSE) located upstream of position -40 relative to the transcription start site. There is little or no existent knowledge concerning the PSE-binding proteins of organisms other than human. Here, we report the purification of a fraction enriched in the Drosophila melanogaster PSE-binding protein (DmPBP). DmPBP forms a highly specific complex with the PSE. The protein stimulates transcription from the U1 gene promoter by RNA polymerase II and from the U6 gene promoter by RNA polymerase III in Drosophila nuclear extracts, and activation is dependent upon the presence of a PSE. The molecular mass of native DmPBP as measured by gel-filtration chromatography is 375 kDa. Two polypeptides (apparent molecular masses 59 kDa and 61 kDa) appear to be in close contact with the DNA in that they can be very efficiently and specifically crosslinked to the PSE sequence by ultraviolet irradiation.

Animals↗
PubMed1994

Structural requirements of Bacillus subtilis small cytoplasmic RNA for cell growth, sporulation, and extracellular enzyme production.

Bacillus subtilis small cytoplasmic RNA (scRNA; 271 nucleotides) is a member of the signal recognition particle (SRP) RNA family, which has evolutionarily conserved primary and secondary structures. The scRNA consists of three domains corresponding to domains I, II, and IV of human SRP 7S RNA. To identify the structural determinants required for its function, we constructed mutant scRNAs in which individual domains or conserved nucleotides were deleted, and their importance was assayed in vivo. The results demonstrated that domain IV of scRNA is necessary to maintain cell viability. On the other hand, domains I and II were not essential for vegetative growth but were preferentially required for the RNA to achieve its active structure, and assembled ribonucleoprotein between Ffh and scRNA is required for sporulation to proceed. This view is highly consistent with the fact that the presence of domains I and II is restricted to sporeforming B. subtilis scRNA among eubacterial SRP RNA-like RNAs.

Bacillus subtilis↗
PubMed1993

An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene.

Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.

Base Sequence↗
PubMed1989

Direct, sequence-specific binding of the human U1-70K ribonucleoprotein antigen protein to loop I of U1 small nuclear RNA.

We have studied the interaction of two of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins, U1-70K and U1-A, with U1 small nuclear RNA (snRNA). The U1-70K protein is a U1-specific RNA-binding protein. Deletion and mutation analyses of a beta-galactosidase/U1-70K partial fusion protein indicated that the central portion of the protein, including the RNP sequence domain, is both necessary and sufficient for specific U1 snRNA binding in vitro. The highly conserved eight-amino-acid RNP consensus sequence was found to be essential for binding. Deletion and mutation analyses of U1 snRNA showed that both the U1-70K fusion protein and the native HeLa U1-70K protein bound directly to loop I of U1 snRNA. Binding was sequence specific, requiring 8 of the 10 bases in the loop. The U1-A snRNP protein also interacted specifically with U1 snRNA, principally with stem-loop II.

Amino Acid Sequence↗