Analysis abstract
Nature Biotechnology 27, 549 - 555 (2009)
Published online: 24 May 2009 | Corrected online: 8 July 2009 | doi:10.1038/nbt.1543
There is a Corrigendum (July 2009) associated with this Analysis.
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
Aly A Khan1,2, Doron Betel2, Martin L Miller2,3, Chris Sander2, Christina S Leslie2,5 & Debora S Marks4,5
Abstract
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.
- Department of Computer Science, Columbia University, New York, New York, USA.
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
- The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
- These authors contributed equally to this work.
Correspondence to: Christina S Leslie2,5 e-mail: cleslie@cbio.mskcc.org
Correspondence to: Debora S Marks4,5 e-mail: deboramarks@gmail.com
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