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. 2004 Jan;10(1):12-8.
doi: 10.1261/rna5160904.

Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs)

Stephan P Persengiev  1 , Xiaochun Zhu, Michael R Green
Affiliations

Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs)

Stephan P Persengiev et al. RNA. 2004 Jan.

Abstract

RNA interference is an evolutionarily conserved process in which expression of a specific gene is post-transcriptionally inhibited by a small interfering RNA (siRNA), which recognizes a complementary mRNA and induces its degradation. Currently, RNA interference is being used extensively to inhibit expression of specific genes for experimental and therapeutic purposes. For applications in mammalian cells, siRNAs are designed to be <approximately 30 base pairs to avoid nonspecific effects that arise from inducing the cellular double-stranded RNA (dsRNA)-dependent protein kinase (PKR) response. Here we perform expression profiling in mammalian tissue-culture cells treated under standard conditions with conventional 21-bp siRNAs and find, unexpectedly, that >1000 genes involved in diverse cellular functions are nonspecifically stimulated or repressed. The effects on gene expression are dependent upon siRNA concentration and are stable throughout the course of siRNA treatment. Our results can be explained by previous studies showing that dsRNAs can affect multiple signaling and transcription pathways in addition to PKR. The potential for this widespread, nonspecific effect on mammalian gene expression must be carefully considered in the design of siRNA experiments and therapeutic applications.

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Figures

FIGURE 1.
FIGURE 1.
Analysis of siRNA-induced alterations in gene expression by RT-PCR. (A) Representative set of up-regulated genes (left) or down-regulated genes (right) after treatment of HeLa cells with transfection reagent (Oligofectamine) alone or with luciferase siRNA. Untreated HeLa cells were used as a control. Fold differences in expression as measured by RT-PCR is indicated on the right. (B) siRNA-induced alteration in gene expression is independent of siRNA sequence. Comparison of luciferase siRNA and a random nonspecific siRNA on the expression of a selected set of stimulated genes (left) or repressed genes (right). Oligofectamine-treated cells were used as a control.
FIGURE 2.
FIGURE 2.
Concentration-dependence and kinetics of siRNA-induced alteration in gene expression. (A) Concentration-dependence. Comparison of varying concentrations of luciferase siRNA on the expression of a selected set of genes. (B) Kinetics. Time-course analysis by RT-PCR of selected genes with expression that increased or decreased after luciferase siRNA treatment.
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References

    1. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., and Struhl, K. 2001. Current protocols in molecular biology. Wiley, New York.
    1. Bridge, A.J., Pebernard, S., Ducraux, A., Nicoulaz, A.L., and Iggo, R. 2003. Induction of an interferon response by RNAi vectors in mammalian cells. Nat. Genet. 34: 263–264. - PubMed
    1. Caplen, N.J., Parrish, S., Imani, F., Fire, A., and Morgan, R.A. 2001. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc. Natl. Acad. Sci. 98: 9742–9747. - PMC - PubMed
    1. Chu, W.M., Ostertag, D., Li, Z.W., Chang, L., Chen, Y., Hu, Y., Williams, B., Perrault, J., and Karin, M. 1999. JNK2 and IKKβ are required for activating the innate response to viral infection. Immunity 11: 721–731. - PubMed
    1. Cole, K.E., Strick, C.A., Paradis, T.J., Ogborne, K.T., Loetscher, M., Gladue, R.P., Lin, W., Boyd, J.G., Moser, B., Wood, D.E., et al. 1998. Interferon-inducible T cell α chemoattractant (I-TAC): A novel non-ELR CXC chemokine with potent activity on activated T cells through selective high affinity binding to CXCR3. J. Exp. Med. 187: 2009–2021. - PMC - PubMed

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