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

UMMS Affiliation

Howard Hughes Medical Institute, Program in Molecular Medicine; Program in Gene Function and Expression

Publication Date


Document Type



Gene Expression Profiling; Gene Expression Regulation; *Gene Silencing; Hela Cells; Humans; Luciferases; Oligonucleotide Array Sequence Analysis; *RNA Interference; RNA, Double-Stranded; RNA, Neoplasm; RNA, Small Interfering; Reverse Transcriptase Polymerase Chain Reaction; Transcription, Genetic


Life Sciences | Medicine and Health Sciences


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 (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.


RNA. 2004 Jan;10(1):12-8.

Journal/Book/Conference Title

RNA (New York, N.Y.)

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Link to Article in PubMed

PubMed ID