Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs Journal Article
| Authors: | Khan, A. A.; Betel, D.; Miller, M. L.; Sander, C.; Leslie, C. S.; Marks, D. S. |
| Article Title: | Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs |
| 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. © 2009 Nature America, Inc. All rights reserved. |
| Keywords: | controlled study; human cell; microrna; gene expression; gene expression profiling; cell line; small interfering rna; rna, small interfering; genetic transcription; cell line, tumor; transfection; rna; gene expression regulation; genetic transfection; quantitative analysis; nucleic acids; binding site; models, genetic; up-regulation; transfer rna; micrornas; genetic screening; rna-induced silencing complex; statistics, nonparametric; short hairpin rna; gene knockdown techniques; gene regulations; human cells; saturation effects; short hairpin rna (shrna); small rna; target prediction; temporal dependence; competition; machinery; binding competition; functional genomics; rna binding; rna transport; genes, cdc |
| Journal Title: | Nature Biotechnology |
| Volume: | 27 |
| Issue: | 6 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2009-06-01 |
| Start Page: | 549 |
| End Page: | 555 |
| Language: | English |
| DOI: | 10.1038/nbt.1543 |
| PUBMED: | 19465925 |
| PROVIDER: | scopus |
| PMCID: | PMC2782465 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 32" - "Export Date: 30 November 2010" - "CODEN: NABIF" - "Source: Scopus" |
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