Rapid match-searching for gene silencing assessment

Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions

The success of RNA interference (RNAi) depends on the interaction between short interference RNAs (siRNAs) and mRNAs. Design of highly efficient and specific siRNAs has become a challenging issue in applications of RNAi. Here, we present a detailed survey on the state-of-the-art siRNAs design, focusing on several key issues with the current in silico RNAi studies, including: (i) inconsistencies among the proposed guidelines for siRNAs design and the incomplete list of siRNAs features, (ii) improper integration of the heterogeneous cross-platform siRNAs data, (iii) inadequate consideration of the binding specificity of the target mRNAs and (iv) reduction in the 'off-target' effect in siRNAs design. With these considerations, the popular in silico siRNAs design rules are reexamined and several inconsistent viewpoints toward siRNAs feature identifications are clarified. In addition, novel computational models for siRNAs design using state-of-art machine learning techniques are discussed, which focus on heterogeneous data integration, joint feature selection and customized siRNAs screening toward highly specific targets. We believe that addressing such issues in siRNA study will provide new clues for further improved design of more efficient and specific siRNAs in RNAi.

Modification of Seed Oil Composition in Arabidopsis by Artificial microRNA-Mediated Gene Silencing

Various post transcriptional gene silencing strategies have been developed and exploited to study gene function or engineer disease resistance. The recently developed artificial microRNA strategy is an alternative method of effectively silencing target genes. The Δ12-desaturase (FAD2), Fatty acid elongase (FAE1), and Fatty acyl-ACP thioesterase B (FATB) were targeted with amiR159b-based constructs in Arabidopsisthaliana to evaluate changes in oil composition when expressed with the seed-specific Brassica napus truncated napin (FP1) promoter. Fatty acid profiles from transgenic homozygous seeds reveal that the targeted genes were silenced. The down-regulation of the AtFAD-2 gene substantially increased oleic acid from the normal levels of ∼15% to as high as 63.3 and reduced total PUFA content (18:2(Δ9,12) + 18:3(Δ9,12,15) + 20:2(Δ11,14) + 20:3(Δ11,14,17)) from 46.8 to 4.8%. Δ12-desaturase activity was reduced to levels as low as those in the null fad-2-1 and fad-2-2 mutants. Silencing of the FAE1 gene resulted in the reduction of eicosenoic acid (20:1(Δ11)) to 1.9 from 15.4% and silencing of FATB resulted in the reduction of palmitic acid (16:0) to 4.4% from 8.0%. Reduction in FATB activity is comparable with a FATB knock-out mutant. These results demonstrate for the first time amiR159b constructs targeted against three endogenous seed-expressed genes are clearly able to down-regulate and generate genotypic changes that are inherited stably over three generations.

Survivin expression in human lung cancer and the influence of its downregulation on the biological behavior of human lung cancer cells

The aim of the present study was to detect the expression of survivin in human lung cancer and to investigate the influence of its downregulation on the biological behavior of A549 lung cancer cells. The high expression of survivin in human lung cancer was verified by immunohistochemistry. Survivin small interfering RNA (siRNA) and unrelated sequence were synthesized and the siRNA lentiviral vector was constructed. The vector was transfected into A549 lung cancer cells, in which the clone with stable expression was screened out. We blocked the expression of survivin mRNA and protein by RNA interference (RNAi) technique. The downregulation of survivin mRNA and protein expression was confirmed by real-time quantitative PCR and western blotting. The proliferative activity and growth rate of A549 cells were determined by colony formation assay and mononuclear cell direct cytotoxicity assay (MTT assay). The reconstituted basement membrane (RBM) penetrating capacity was determined by cell invasion assay. The cell movement and migratory capacity were detected by wound-healing repair assay. The results showed that the sequence-specific siRNA significantly downregulated the expression of survivin at both the mRNA and protein levels. Downregulation of survivin expression dramatically decreased the invasive and metastatic capacities of the cells, suppressed the proliferation, decelerated the rate of growth, reduced the number of clones on soft agar and decreased the capacity of RBM penetration and migration. In conclusion, survivin, which plays an important role in carcinogenesis and development of lung cancer, can be effectively downregulated using the RNAi technique.

Effects and mechanism of downregulation of survivin expression by RNA interference on proliferation and apoptosis of lung cancer cells

The survivin protein, a member of the inhibitors of apoptosis (IAP) family, has gained popularity as a therapeutic target for cancer due to its selective expression in tumor cells and its significant involvement in tumor cell viability. The aim of this study was to investigate the effect of the survivin-small interfering RNA (siRNA) plasmid on survivin expression in the human lung cancer cell line, A549, and to observe its effects on apoptosis and proliferation of A549 cells. A549 human lung cancer cells were transfected with survivin-targeting siRNA. The downregulation of survivin expression was determined by real-time polymerase chain reaction and western blotting. The proliferation of A549 cells was determined by MTT assay. The apoptotic rate and cell cycle distribution were analyzed by flow cytometry (FCM). Caspase-9 activity was also detected to study the apoptosis of lung cancer cells induced by siRNA against survivin. The sequence-specific siRNA efficiently and specifically downregulated the expression of survivin at both the mRNA and protein levels. Downregulation of survivin expression dramatically suppressed the proliferation of A549 cells and arrested the cells at the G (1)/G (0) phase. Caspase-9 activity was significantly increased in A549 cells transfected with siRNA against survivin. In this study, we found that survivin-specific siRNA can efficiently suppress the expression of survivin, increase apoptosis and inhibit A549 cell proliferation. Our findings further indicate the possibility that the antitumor effects of survivin-siRNA are mediated through the activation of caspase-9.