Gene expression silencing with 'specific' small interfering RNA goes beyond specificity: a study of key parameters to take into account in the onset of small interfering RNA off-target effects

Sebastien Vankoningsloo, Françoise De Longueville, Stephanie Evrard, Pierre Rahier, Andrée Houbion, Antoine Fattaccioli, Mélanie Piette Gastellier, José Remacle, Martine Raes, Patricia Renard, Thierry Arnould

Research output: Contribution to journalArticle

Abstract

RNA-mediated gene silencing (RNA interference) is a powerful way to knock down gene expression and has revolutionized the fields of cellular and molecular biology. Indeed, the transfection of cultured cells with small interfering RNAs (siRNAs) is currently considered to be the best and easiest approach to loss-of-function experiments. However, several recent studies underscore the off-target and potential cytotoxic effects of siRNAs, which can lead to the silencing of unintended mRNAs. In this study, we used a low-density microarray to assess gene expression modifications in response to five different siRNAs in various cell types and transfection conditions. We found major differences in off-target signature according to: (a) siRNA sequence; (b) cell type; (c) duration of transfection; and (d) post-transfection time before analysis. These results contribute to a better understanding of important parameters that could impact on siRNA side effects in knockdown experiments.
Original languageEnglish
Pages (from-to)2738-2753
Number of pages16
Journal FEBS Journal
Volume275
Issue number11
Publication statusPublished - 2008

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Gene Silencing
Gene expression
Small Interfering RNA
Transfection
Gene Expression
Cytology
RNA
Molecular biology
Microarrays
RNA Interference
Cell Biology
Molecular Biology
Cultured Cells
Genes
Experiments
Cells
Messenger RNA

Cite this

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title = "Gene expression silencing with 'specific' small interfering RNA goes beyond specificity: a study of key parameters to take into account in the onset of small interfering RNA off-target effects",
abstract = "RNA-mediated gene silencing (RNA interference) is a powerful way to knock down gene expression and has revolutionized the fields of cellular and molecular biology. Indeed, the transfection of cultured cells with small interfering RNAs (siRNAs) is currently considered to be the best and easiest approach to loss-of-function experiments. However, several recent studies underscore the off-target and potential cytotoxic effects of siRNAs, which can lead to the silencing of unintended mRNAs. In this study, we used a low-density microarray to assess gene expression modifications in response to five different siRNAs in various cell types and transfection conditions. We found major differences in off-target signature according to: (a) siRNA sequence; (b) cell type; (c) duration of transfection; and (d) post-transfection time before analysis. These results contribute to a better understanding of important parameters that could impact on siRNA side effects in knockdown experiments.",
author = "Sebastien Vankoningsloo and {De Longueville}, Fran{\cc}oise and Stephanie Evrard and Pierre Rahier and Andr{\'e}e Houbion and Antoine Fattaccioli and Gastellier, {M{\'e}lanie Piette} and Jos{\'e} Remacle and Martine Raes and Patricia Renard and Thierry Arnould",
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T1 - Gene expression silencing with 'specific' small interfering RNA goes beyond specificity: a study of key parameters to take into account in the onset of small interfering RNA off-target effects

AU - Vankoningsloo, Sebastien

AU - De Longueville, Françoise

AU - Evrard, Stephanie

AU - Rahier, Pierre

AU - Houbion, Andrée

AU - Fattaccioli, Antoine

AU - Gastellier, Mélanie Piette

AU - Remacle, José

AU - Raes, Martine

AU - Renard, Patricia

AU - Arnould, Thierry

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AB - RNA-mediated gene silencing (RNA interference) is a powerful way to knock down gene expression and has revolutionized the fields of cellular and molecular biology. Indeed, the transfection of cultured cells with small interfering RNAs (siRNAs) is currently considered to be the best and easiest approach to loss-of-function experiments. However, several recent studies underscore the off-target and potential cytotoxic effects of siRNAs, which can lead to the silencing of unintended mRNAs. In this study, we used a low-density microarray to assess gene expression modifications in response to five different siRNAs in various cell types and transfection conditions. We found major differences in off-target signature according to: (a) siRNA sequence; (b) cell type; (c) duration of transfection; and (d) post-transfection time before analysis. These results contribute to a better understanding of important parameters that could impact on siRNA side effects in knockdown experiments.

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