A novel bidirectional expression system for simultaneous expression of both the protein-coding genes and short hairpin RNAs in mammalian cells

Bidirectional promoters in the transcription of mammalian genomes

In the genomes of humans and other mammals a large number of closely spaced pairs of genes that are transcribed in opposite directions were revealed. Their transcription is directed by so-called bidirectional promoters. This review is devoted to the characteristics of bidirectional promoters and features of their structure. The composition of "core" promoter elements in conventional unidirectional and bidirectional promoters is compared. Data on binding sites of transcription factors that are primarily specific for bidirectional promoters are discussed. The examples of promoters that share protein-coding genes transcribed by RNA polymerase II and the non-coding RNA genes transcribed by RNA polymerase III are described. Data obtained from global transcriptome analysis about the existence of short noncoding antisense RNA associated with the promoters in the context of the hypothesis of bidirectional transcription initiation as an inherent property of eukaryotic promoters are discussed.

Construction of multiple shRNAs expression vector that inhibits FUT1 gene expression and production of the transgenic SCNT embryos in vitro

Enterotoxigenic Escherichia coli F18 is a major pathogen that causes postweaning diarrhoea and edema disease in piglets. The alpha(1,2)-fucosyltransferase (FUT1) gene has been identified as an ideal candidate gene for controlling the expression of the receptor for ECF18 bacteria. Therefore, the use of RNA interference (RNAi) to study the function of the FUT1 gene and to produce FUT1 knockdown transgenic pig would be highly beneficial. We developed an effective strategy for the expression of multiple small hairpin RNA simultaneously using multiple RNA polymerase III (hU6, hH1, mU6 and h7SK) promoters in a single vector to knockdown the FUT1 gene. Stable FUT1 knockdown transgenic fibroblast lines were generated by transfecting porcine fetal fibroblasts with the constructed vectors. Real-time RT-PCR indicated that the mRNA level of FUT1 in the transgenic fibroblast lines was significantly lower than that in the control, as much as 29 %. Finally, we successfully obtained transgenic SCNT porcine embryos. Overall, the results demonstrated that this vector-based RNAi expression system is an efficient approach to knockdown FUT1 gene expression in porcine fetal fibroblast cells, which could thereby provide donor cells for somatic cell nuclear cloning and the potential production of a marker-free transgenic pig resistant to F18 related diseases. Furthermore, it also provides strong evidence that this approach could be useful both in the production of transgenic livestock resistant to disease, and in the development of effective strategies for the suppression of gene expression in clinical gene therapy.

The Sound of Silence: RNAi in Poly (ADP-Ribose) Research

Poly(ADP-ribosyl)-ation is a nonprotein posttranslational modification of proteins and plays an integral part in cell physiology and pathology. The metabolism of poly(ADP-ribose) (PAR) is regulated by its synthesis by poly(ADP-ribose) polymerases (PARPs) and on the catabolic side by poly(ADP-ribose) glycohydrolase (PARG). PARPs convert NAD+ molecules into PAR chains that interact covalently or noncovalently with target proteins and thereby modify their structure and functions. PAR synthesis is activated when PARP1 and PARP2 bind to DNA breaks and these two enzymes account for almost all PAR formation after genotoxic stress. PARG cleaves PAR molecules into free PAR and finally ADP-ribose (ADPR) moieties, both acting as messengers in cellular stress signaling. In this review, we discuss the potential of RNAi to manipulate the levels of PARPs and PARG, and consequently those of PAR and ADPR, and compare the results with those obtained after genetic or chemical disruption.

Nonvariceal upper gastrointestinal bleeding: the usefulness of rotational angiography after endoscopic marking with a metallic clip

Objective

We wanted to assess the usefulness of rotational angiography after endoscopic marking with a metallic clip in upper gastrointestinal bleeding patients with no extravasation of contrast medium on conventional angiography.

Materials and Methods

In 16 patients (mean age, 59.4 years) with acute bleeding ulcers (13 gastric ulcers, 2 duodenal ulcers, 1 malignant ulcer), a metallic clip was placed via gastroscopy and this had been preceded by routine endoscopic treatment. The metallic clip was placed in the fibrous edge of the ulcer adjacent to the bleeding point. All patients had negative results from their angiographic studies. To localize the bleeding focus, rotational angiography and high pressure angiography as close as possible to the clip were used.

Results

Of the 16 patients, seven (44%) had positive results after high pressure angiography as close as possible to the clip and they underwent transcatheter arterial embolization (TAE) with microcoils. Nine patients without extravasation of contrast medium underwent TAE with microcoils as close as possible to the clip. The bleeding was stopped initially in all patients after treatment of the feeding artery. Two patients experienced a repeat episode of bleeding two days later. Of the two patients, one had subtle oozing from the ulcer margin and that patient underwent endoscopic treatment. One patient with malignant ulcer died due to disseminated intravascular coagulation one month after embolization. Complete clinical success was achieved in 14 of 16 (88%) patients. Delayed bleeding or major/minor complications were not noted.

Conclusion

Rotational angiography after marking with a metallic clip helps to localize accurately the bleeding focus and thus to embolize the vessel correctly.

Dual transgene expression by foamy virus vectors carrying an endogenous bidirectional promoter

Several gene therapy applications require the transfer and simultaneous expression of multiple genes in the same cell. In this study, we analyzed the potential for coordinated expression of an endogenous bidirectional promoter located on chromosome X, which controls the expression of the heterogeneous nuclear ribonucleoprotein H2 (HNRNPH2) and alpha-galactosidase (GLA) genes. The promoter was cloned in both transcriptional orientations in a foamy virus (FV) vector backbone, whereas the enhanced green fluorescent protein (EGFP) and low-affinity nerve growth factor receptor (DeltaLNGFR) reporter genes were cloned in the 5'-3' and 3'-5' transcriptional orientations, respectively. In all the cell lines tested, both vectors showed high levels of transgene coexpression that reached 76% of total positive cells (range from 76 to 18%). Comparison of EGFP and DeltaNGFR levels revealed that the side of the promoter that drives the expression of the HNRNPH2 gene in the genome was stronger and in accordance to its in situ activity. When tested with CD34(+) cells, transgene coexpression reached 35.3% of all positive cells in progenitor assays and 16.8% of all positive cells after transplantation in NOD/severe combined immunodeficient mice. In summary, we show that the endogenous promoter used in this study holds bidirectional activity in the context of FV vectors and can be used in gene therapy applications requiring synchronized expression of two genes.

A novel approach for the construction of multiple shRNA expression vectors

The application of RNA interference (RNAi) as a research and therapeutic tool depends on its ability to silence genes in a sequence-specific manner. Recent studies have reported that the effective knockdown of genes can be achieved by multiple short hairpin RNAs (shRNAs) in a single vector. Moreover, this approach can depress several genes simultaneously. However, current methods for the construction of multiple shRNA vectors often suffer from vector instability and are time-consuming. Here, we describe a simple, quick and low-cost approach to construct a single vector expressing four shRNA sequences driven by four different promoters. Using this vector, we were able to improve the gene silencing efficiency and make it possible to silence four different genes simultaneously, further expanding the application spectrum of RNAi, both in functional studies and therapeutic strategies.

A novel shRNA vector that enables rapid selection and identification of knockdown cells

Small interference RNA (siRNA) is a powerful tool for disrupting expression of specific genes in a variety of cells. We have developed a vector, piMARK, which mediates expression of both small hairpin RNA (shRNA) and the blasticidin resistance (Bsr) protein fused with enhanced green fluorescent protein (EGFP), enabling rapid selection and identification of knockdown cells. Using this vector, we targeted Ect2, a gene encoding a guanine nucleotide exchange factor for several small GTPases, in human cell lines. Incubation in the presence of 10 microg/ml blasticidin S rapidly killed untransfected cells, so that after 24 h >90% of surviving HeLa S3 cells emitted green fluorescence and >70% were binucleate as a result of the frequent failure of cell division. The GFP-Bsr fluorescence enabled easy identification of individual knockdown cells under a fluorescence microscope, which in turn enabled unambiguous assessment of the morphological consequences of silencing Ect2. Moreover, because untransfected cells rapidly died and detached from the substrate, they were easily removed by simply rinsing the culture dishes. It thus should be possible to analyze the biochemical consequences of gene silencing en masse in the absence of a background of untransfected cells.

Construction of simple and efficient DNA vector-based short hairpin RNA expression systems for specific gene silencing in mammalian cells

RNA interference (RNAi) is an evolutionarily conserved mechanism of posttranscriptional gene silencing induced by introducing the double-stranded RNAs (dsRNAs) into cells. Recent progress in RNAi-based gene-silencing techniques has revolutionarily advanced in studies of the functional genomics and molecular therapeutics. Among the widely used dsRNAs including exogenously synthetic and endogenously expressed small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs), the shRNAs are more efficient than siRNAs on the induction of gene silencing and currently have evolved as an extremely powerful and the most popular gene silencing reagent. The DNA vector-based shRNA-expression systems provide not only a simple and effective way in inhibiting gene activities in either inheritable or inducible manner, but also a cost-effective tool in constructing the expression vectors. To fully explore the DNA vector-based shRNA-expression systems in RNAi-mediated gene-silencing techniques, four distinct RNA polymerase III (Pol III)-controlled type III promoter-based expression vectors are constructed including pHsH1, pHsU6, pMmH1, and pMmU6, which contain either the RNase P RNA H1 (H1) or small nuclear RNA U6 (U6) promoter from human and mouse. Moreover, to improve the constructing and screening efficiency for the shRNA-expression recombinant clones, these four DNA vectors are further reconstructed by inserting a stuffer of puromycin resistance gene (PuroR) between restriction enzyme ClaI and HindIII sites, which makes the preparation of vectors easy and simple for cloning the shRNA-expression sequences. Because of the ease, speed, and cost efficiency, these four improved DNA vector-based shRNA-expression vectors provide a simple, convenient, and efficient gene-silencing system for analyzing specific gene functions in mammalian cells. Herein, the simple and practical procedures for the construction of DNA vector-based expression vectors, potential and rational design rules for the selection of effective RNAi-targeting sequences, efficient and cost-effective cloning strategies for the construction of shRNA-expression cassettes, and effective and functional activity assays for the evaluation of expressed shRNAs are described.