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[资源] Transfection of small RNAs globally perturbs gene regulation by

Transfection of small RNAs (such as small interfering RNAs
(siRNAs) and microRNAs (miRNAs)) into cells typically lowers
expression of many genes. Unexpectedly, increased expression
of genes also occurs. We investigated whether this
upregulation results from a saturation effect—that is,
competition among the transfected small RNAs and the
endogenous pool of miRNAs for the intracellular machinery
that processes small RNAs. To test this hypothesis, we
analyzed genome-wide transcript responses from 151
published transfection experiments in seven different human
cell types. We show that targets of endogenous miRNAs are
expressed at significantly higher levels after transfection,
consistent with impaired effectiveness of endogenous miRNA
repression. This effect exhibited concentration and temporal
dependence. Notably, the profile of endogenous miRNAs can
be largely inferred by correlating miRNA sites with gene
expression changes after transfections. The competition and
saturation effects have practical implications for miRNA target
prediction, the design of siRNA and short hairpin RNA
(shRNA) genomic screens and siRNA therapeutics.

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