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PubMedDate not supplied

Cytotoxic ribonucleases and RNA interference (RNAi).

Several cytotoxic ribonucleases (CRs), homologs of the pancreatic RNase A, have been isolated from amphibian oocytes or embryos. Of them, onconase (Onc), the CR that shows antitumor properties and is in phase III clinical trials, was the most extensively researched. Degradation of tRNA by Onc internalized into cells that leads to inhibition of protein synthesis is considered the mechanism of its cytotoxicity. Several findings, however, cannot be explained by nonspecific decline in protein synthesis alone and suggest additional or alternative mechanism(s). We postulate therefore that miRNAs and/or RNA interference (RNAi) may also be targets of CRs. The following arguments support this postulate: (A) miRNAs and siRNAs appear to be unprotected by proteins and therefore, as tRNA, accessible and degradable by CRs; (B) Onc has preferred cleavage sites on tRNAs: their cleavage may generate segments of dsRNA that interfere with translation. Analogous to Dicer, thus, small RNAs with interfering properties may be generated by CRs within the cell; (C) CRs are abundant in oocytes and during embryonic development; their role there is unknown. Since cells undergo perpetual differentiation during embryogenesis it is likely that the function of CRs is to provide additional level of regulation of gene expression via the mechanisms listed in (A) and/or (B).

Animals↗
PubMed2005

Specific RNAi mediated gene knockdown in zebrafish cell lines.

Here we demonstrate highly efficient RNA interference in ZFL, SJD and ZF4 cell lines derived from adult and embryonic zebrafish Danio rerio. Microinjection of siRNAs resulted in silencing in almost 100% of cells while transfection using cationic liposomes led to silencing in 30%. Use of siRNAs against zebrafish lamin A, lamin B2 and the motor protein Eg5, led to knockdown of the target genes with the specific phenotypes expected from prior studies in mammalian cells. In contrast injection of lamin A, GL2 and eGFP siRNAs into zebrafish embryos resulted in morphological defects, abnormal development and early death of most embryos. The results indicate unspecific responses to siRNAs in the embryo but a fully developed and active RNAi machinery in cell lines.

Animals↗
PubMed2005

A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation.

The assembly of heterochromatin in fission yeast and metazoans requires histone H3-lysine 9 (-K9) methylation by the conserved Clr4/Suv39h methyltransferase. In fission yeast, H3-K9 methylation requires components of the RNAi machinery and is initiated by the RNA-Induced Transcriptional Silencing (RITS) complex. Here we report the purification of a novel complex that associates with the Clr4 methyltransferase, termed the CLRC (CLr4-Rik1-Cul4) complex. By affinity purification of the Clr4-associated protein Rik1, we show that, in addition to Clr4, Rik1 is associated with the fission yeast E3 ubiquitin ligase Cullin4 (Cul4, encoded by cul4(+)), the ubiquitin-like protein, Ned8, and two previously uncharacterized proteins, designated Cmc1 and Cmc2. In addition, the complex contains substochiometric amounts of histones H2B and H4, and the 14-3-3 protein, Rad24. Deletion of cul4(+), cmc1(+), cmc2(+) and rad24(+) results in a complete loss of silencing of a ura4(+) reporter gene inserted within centromeric DNA repeats or the silent mating type locus. Each of the above deletions also results in accumulation of noncoding RNAs transcribed from centromeric repeats and telomeric DNA regions, and a corresponding loss of small RNAs that are homologous to centromeric repeats, suggesting a defect in the processing of noncoding RNA to small RNA. Based on these results, we propose that the components of the Clr4-Rik1-Cul4 complex act concertedly at an early step in heterochromatin formation.

Cell Cycle Proteins↗
PubMed2004

[A DNA vector-based RNAi technology to inhibit the activity of the telomerase of cell line HCCLM3].

OBJECTIVE: To develop a DNA vector-based RNA interference (RNAi) technology that inhibits the activity of the telomerase of the hepatocellular carcinoma cell line HCCLM3 in order to suppress the proliferation of the cells. METHODS: Hepatocellular carcinoma cells of the line HCCLM3 were cultured. mRNA interfering double-stranded DNA vector PSG-AS targeting the mRNA of human telomerase reverse transcriptase (hTERT) and the control vector PSG-CTR were constructed respectively, and then were transfected into the HCCLM3 cells. The expression of hTERT of the transfected cells was determined by Western blotting and the activity of telomerase was determined by telomeric repeat amplification-ELISA (TRAP-ELISA). Flow cytometry was used to detect the apoptosis of transfected cells and MTS method was used to measure the growth curve of the cells so as to observe the effect of the PSG-AS on the proliferation of HCCLM3 cell. RESULTS: TRAP-ELISA showed that the inhibition rate of PSG-AS on the telomerase activity was 76%. The apoptotic rate of the PSG-AS group was significantly higher than that of the PSG-CTR group (t = 11.48, P < 0.001). Western blotting showed a remarkable inhibition of hTERT protein in the PSG-AS group. CONCLUSION: Capable of suppressing the hTERT expression and the activity of telomerase, RNA interfering technology can be applied to treatment of tumors.

Apoptosis↗
PubMed2005

Reduction of Pnn by RNAi induces loss of cell-cell adhesion between human corneal epithelial cells.

PURPOSE: Pinin (Pnn/DRS/memA) plays an important role in regulating cell-cell adhesion of corneal epithelial cells. In the nucleus, Pnn interacts with both transcriptional repressor and pre-mRNA processing machinery. Here we investigated the consequences of "knocking down" Pnn expression with short hairpin RNAi (shRNAi) on the corneal epithelial cell phenotype. METHODS: Cultured human corneal epithelial (HCE-T) cells were cotransfected with a shRNAi-expressing construct containing an inverted repeat of a Pnn specific 21 nucleotide sequence (Pnn shRNAi) and a GFP vector as a marker of transfected cells. After 24-48 h, cells were fixed and immunostained with antibodies against Pnn, keratin, desmoplakin, desmoglein, E-cadherin, ZO-1, SR-proteins, and SRm300. To demonstrate specificity of the Pnn knock down, a rescue vector was designed by incorporating three conservative nucleotide substitutions within the Pnn-shRNAi targeting sequences of the full length Pnn-GFP construct, thus generating a Pnn construct to produce mRNA that Pnn shRNAi could not target (Pnn-CS3-GFP). RESULTS: HCE-T cells were cotransfected with Pnn shRNAi and GFP vectors and after 24 and 48 h exhibited significantly reduced immunostaining for Pnn. Western blot analyses of Pnn and E-cadherin protein expression in cells transfected with Pnn-shRNAi and GFP vectors revealed marked reduction in levels of both proteins compared to those observed in cells transfected with GFP alone. The cells receiving Pnn-shRNAi appeared to be less adherent to neighboring nontransfected cells, often exhibited altered cell shape, downregulated cell adhesion and cell junction molecules, and escaped from the epithelium. The Pnn shRNAi transfected cells exhibited fewer keratin filaments anchored to desmosomes and a concurrent increase in the perinuclear bundling of filaments. SR proteins and SRm300 showed an altered distribution in the Pnn knock down cells. Cotransfection of Pnn-CS3-GFP with Pnn shRNAi demonstrated that the conservatively mutated Pnn could maintain cell-cell adhesion. CONCLUSIONS: Our results indicate that knocking down Pnn expression leads to a loss of epithelial cell-cell adhesion, changes in cell shape, and movement of Pnn shRNAi transfected cells out of the epithelium. We suggest that Pnn plays an integral role in the establishment and maintenance of epithelial cell-cell adhesion via its activity within nuclear multi-protein complexes.

Blotting, Western↗
PubMed2005

[Cloning of ACC oxidase gene and inhibition of endogenous gene expression with RNAi in cauliflower].

A fragment of 1202 bp of the candidate ACO gene was amplified from the cauliflower (brassica oleracea Var. botrytis) genome using the degenerated primers which were designed according to the consensus sequence of ACO amino acids among various plant species. The result of BLAST showed the sequence presented a very high match with the ACO genes from other plants; the homologue was from 83% to 99%. Three exons and two introns were identified in this sequence. The spliced length of mRNA was 756 nt and encoded 252 amino acids. The putative new gene was denominated BoACO, and submitted to GenBank (AY676466). Using the sequence, we constructed an RNA interference (RNAi) transformation vector through the way of BP cloning. The transformation into cauliflower was performed. Five regenerated plants with kanamycin resistance were obtained. And the transgene integrated into cauliflower genome was proved with PCR and Southern blotting. The expression of this ACO gene is down-regulated based on the Northern blotting in the transgenic plants. The activity of ACO enzyme was depressed significantly.

Amino Acid Oxidoreductases↗
PubMed2005

[Effect of RNAi-mediated gene silencing of C-erbB-2 on proliferation of lung adenocarcinoma cell line calu-3].

BACKGROUND & OBJECTIVE: C-erbB-2 gene is amplified or overexpressed in breast cancer, ovarian cancer, and lung cancer, and is related with enhanced malignancy and metastatic ability, intrinsic chemoresistance, and poor prognosis of tumors. RNA interfering (RNAi), a new genetic technique, can efficiently and specifically suppress gene expression. This study was to investigate the effect of small interfering RNA (siRNA)-mediated gene silencing of C-erbB-2 on proliferation of human lung adenocarcinoma cell line calu-3. METHODS: C-erbB-2 siRNA was transfected into calu-3 cells; cell morphology was observed under light microscope. The mRNA and protein levels of C-erbB-2 were detected by reverse transcription-polymerase chain reaction (RT-PCR) and flow cytometry (FCM). The proliferation of calu-3 cells was assessed by MTT assay. Cell cycle and apoptosis were analyzed by FCM. RESULTS: C-erbB-2 siRNA down-regulated the mRNA and protein levels of C-erbB-2 in calu-3 cells; 48 h after transfection of C-erbB-2 siRNA, the protein level of C-erbB-2 was markedly decreased. The positive rate of C-erbB-2 was significantly lower in C-erbB-2 siRNA group than in untransfected group, empty vector group, and nonspecific siRNA group [(25.04+/-1.56)% vs. (98.24+/-2.23)%, (95.67+/-1.98)%, and (94.79+/-0.87)%, P < 0.01]. C-erbB-2 siRNA inhibited proliferation of calu-3 cells: G(0)/G(1) phase proportion of C-erbB-2 siRNA group was significantly higher than that of untransfected group [(56.6+/-3.6)% vs. (45.5+/-3.2)%, P < 0.01]. C-erbB-2 siRNA also enhanced cell apoptosis. CONCLUSION: Specific siRNA targeting C-erbB-2 can effectively inhibit C-erbB-2 expression and proliferation of calu-3 cells.

Adenocarcinoma↗
PubMed2006

[Gene silencing RNAi technology: possible application to therapy].

RNA interference (RNAi), i.e. gene silencing, or gene expression down-regulation is the process whereby a double-stranded RNA (dsRNA) induces the homology-dependent degradation of cognate messenger RNA (mRNA). When dsRNA is introduced into cells, an RNA-induced silencing complex (RISC) is assembled. RISC serves as cellular machinery that is responsible for the specific mRNA degradation. This process results in the subsequent reduction of the specific protein translated from appropriate mRNA. Short RNA duplexes (21 nucleotide), called small interfering RNA (siRNA), have become the major tool for induction of gene silencing. With the human genome mapped and sequenced, attempts are currently being made to manipulate the expression of genes involved in viral diseases, carcinogenesis and other disorders with the aim of developing novel therapies.

Chromosome Mapping↗
PubMed2006

[Inhibition of rat RAW264.7 macrophage inflammatory cytokines release by small hairpin RNAi targeting Toll-like receptor].

OBJECTIVE: To construct a eukaryotic expression vector carrying the small hairpin RNA (shRNA) for Toll-like receptor 4 (TLR4) mRNA and a reporter gene of enhanced green fluorescence protein (EGFP) and study the inhibition of cytokine release by rat RAW264.7 macrophages induced by lipopolysaccharide (LPS) stimulation through transfection and expression of shRNA targeting TLR4 gene via the RNAi mechanism. METHODS: The H1 promotor and double BbsIrestrict endoenzyme site from the plasmid psiRNA-hH1neo were cloned into the reporter gene plasmid pEGFP-C1 at the MluIrestrict endoenzymic site, thus forming the plasmid pEGFP-H1/siRNA containing Bbs site and reporter EGFP gene. Then an oligo nuclear hairpin sequence targeting TLR4 gene was designed by the internet tool siRNA Wizard and then inserted into the plasmid pEGFP-H1/siRNA so as to form the plasmid pEGFP-H1/TLR4-siRNA. Rat macrophages of the line RAW264.7 were cultured and transfected with pEGFP-H1/TLR4-siRNA mediated by lipofectamine 2000. Another RAW264.7 cells were transfected with pEGFP-H1/control sequence-siRNA or blank plasmid. Lipopolysaccharide was added into the 3 kinds of culture fluid for 2 and 68 hours respectively. ELSA was used to detect the levels of tumor necrosis factor-alpha (TNF-alpha) in the supernatants. RESULTS: Restriction endonuclease analysis showed that the construction pEGFP-H1/TLR4-siRNA carrying hairpin RNA for TLR4 gene and reporter EGFP gene was successful. The expression of EGFP gene was 50% +/- 8%. The TNF-alpha level of the TLR4-siRNA transfection group 2 hours and after transfection was 825 pg/ml +/- 136 pg/ml, significantly lower than those of the pEGFP-H1/control sequence-siRNA and blank plasmid groups (2190 pg/ml +/- 359 pg/ml and 1265 pg/ml +/- 283 pg/ml respectively, both P < 0.01). The TNF-alpha level of the TLR4-siRNA transfection group 8 hours and after transfection was 1179 pg/ml +/- 240 pg/ml, significantly lower than those of the pEGFP-H1/control sequence-siRNA and blank plasmid groups (4720 pg/ml +/- 227 pg/ml and 4689 pg/ml +/- 310 pg/ml respectively, both P < 0.01). CONCLUSION: shRNA targeting TLR4 gene can inhibit the TNF-alpha release by RAW264.7 cells evoked by LPS.

Animals↗
PubMed2006

[Selecting the RNAi efficiency target sites of lZP3 gene by mouse in vivo].

As the combining target with sperms, ZP3 undergoes an important role in the fertilization of oocytes and therefore it has been the focus in studying the mechanism of mammalian. According to the sequence of the zona pellucida 3 gene of Lagurus lagurus (lZP3), three RNA interference recombinant vectors were constructed with pGenesil-1 aiming at lZP3 mRNA by synthesizing oligonucleotides. And then co-transfected into the Hela cells by Lipofectamine2000 and co-injected into the mice by hydrodynamics-based transfection method with the expression vector pCDNA3-lZP3. In order to select the efficient target sites of lZP3 for RNAi, the mRNA expression level of lZP3 gene in Hela cells and the mouse liver was detected by semi-quantative RT-PCR and real-time PCR. Results show that there are 2 interference vectors can interfere of the expression of lZP3 mRNA, and the mRNAs of the exogenous genes expressed in the mouse liver are coincident with those of in Hela cells after co-transfected with the interference vectors and expression vector. It also suggests that the mice can be the experimental materials for selecting the efficiency target sites of the RNA interference.

Animals↗
PubMed1989

Identification of a 90-kDa polypeptide which associates with adenovirus VA RNAI and is phosphorylated by the double-stranded RNA-dependent protein kinase.

Interferon treatment of mammalian cells induces a double-stranded (ds) RNA-dependent protein kinase known as DAI. When activated, DAI phosphorylates the alpha-subunit of eukaryotic initiation factor eIF-2, impairing its ability to be recycled and leading to the inhibition of protein synthesis. We have identified a novel DAI substrate in the ribosomal salt wash of rabbit reticulocyte lysates. This substrate is a 90-kDa polypeptide which has been purified to apparent homogeneity. It can be cross-linked by ultraviolet irradiation to adenovirus VA RNAI, a small RNA polymerase III transcript RNA which acts as an inhibitor of DAI. As assayed by a nitrocellulose filter binding assay, the 90-kDa polypeptide is also able to associate with authentic double-stranded RNA, but not single-stranded RNA, made in vitro. Thus, this newly identified substrate of DAI appears to have affinity for dsRNA structures and may be involved in dsRNA-regulated processes in the reticulocyte. Polyclonal and monoclonal antibodies directed against the 90-kDa polypeptide co-precipitate DAI, suggesting that these two proteins may exist as a complex.

Adenoviruses, Human↗
PubMed2017

Future of rAAV Gene Therapy: Platform for RNAi, Gene Editing, and Beyond.

The use of recombinant adeno-associated viruses (rAAVs) ushered in a new millennium of gene transfer for therapeutic treatment of a number of conditions, including congenital blindness, hemophilia, and spinal muscular atrophy. rAAV vectors have remarkable staying power from a therapeutic standpoint, withstanding several ebbs and flows. As new technologies such as clustered regularly interspaced short palindromic repeat genome editing emerge, it is now the delivery tool-the AAV vector-that is the stalwart. The long-standing safety of this vector in a multitude of clinical settings makes rAAV a selling point in the advancement of approaches for gene replacement, gene knockdown, gene editing, and genome modification/engineering. The research community is building on these advances to develop more tailored delivery approaches and to tweak the genome in new and unique ways. Intertwining these approaches with newly engineered rAAV vectors is greatly expanding the available tools to manipulate gene expression with a therapeutic intent.

Dependovirus↗
PubMed2026

Genome-Wide In Vivo RNAi Screening Identifies HOXD4 as a Tumor Metastasis Suppressor in Colorectal Cancer.

Metastasis remains a major therapeutic challenge in colorectal cancer, highlighting an urgent need to elucidate its underlying molecular mechanisms. In this study, an in vivo screening system integrating genome-wide short hairpin RNA library and next-generation sequencing identifies six candidate metastasis suppressors, among which Homeobox D4 (HOXD4) shows the most pronounced effects. Clinicopathological analyses reveal significant HOXD4 downregulation in tumor tissues relative to adjacent normal tissues, with reduced expression strongly correlating with aggressive tumor features. Functional assays demonstrate that HOXD4 depletion enhances migration, invasion, and tumorsphere formation in HCT116 cells, while ectopic HOXD4 overexpression reverses these malignant phenotypes in SW620 cells. Mechanistically, HOXD4 suppresses epithelial-mesenchymal transition (EMT) by directly binding to the promoter of Forkhead box Q1 (FOXQ1), a key driver of EMT and stemness, and thereby transcriptionally repressing its expression. Immunohistochemistry confirms an inverse correlation between HOXD4 and FOXQ1 expression in clinical specimens. Rescue experiments substantiate that HOXD4 exerts its metastasis-suppressing functions via FOXQ1 regulation. Collectively, these findings not only establish an efficient platform for screening tumor metastasis suppressors, but also identify HOXD4 as a master transcriptional regulator of the FOXQ1-EMT axis, providing a promising target for metastasis interception.

Humans↗
PubMed1998

Identification of a new gene in the streptococcal plasmid pLS1: the rnaI gene.

The streptococcal plasmid pMV158 has been reported to harbor five genes: three involved in initiation of rolling circle replication and its control (copG, repB, and maII), one involved in conjugative mobilization (mobM), and the fifth one specifying constitutive resistance to tetracycline (tet). The mobM gene was removed in the construction of the pMV158-derivative plasmid pLS1, which was used in this study. By in vitro transcription assays, primer extension experiments, and construction of mutations, here we demonstrate the presence of another gene (the sixth of pMV158), termed maI, which is transcribed in opposite orientation with respect to the plasmid mRNAs, to render RNA I. The 5'-end of RNA I has an 8-nt sequence which is complementary to a region of the lagging-strand origin (ssoA) comprising a 6-nt consensus sequence involved in lagging strand synthesis. This suggested that RNA I could influence, positively or negatively, initiation of lagging strand synthesis from the pLS1-ssoA. However, plasmids defective in RNA I synthesis exhibited a phenotype similar to the wild type in terms of efficiency of replication from the ssoA and copy number. When the maI gene was cloned into a compatible plasmid, the resulting recombinants did not exhibit incompatibility toward plasmids with the pLS1 replicon. Thus, RNA I does not seem to be a true copy number control element. We postulate that transcription from the maI promoter may facilitate extrusion of the hairpin of the plasmid double-strand origin, which is the target of the initiator of replication protein.

Base Sequence↗