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.
authors.affiliation: Laboratoire de Biochimie et Biologie Cellulaire, University of Namur FUNDP, Belgium.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Vankoningsloo
authors.forename: Françoise
authors.initials: F
authors.lastname: de Longueville
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Evrard
authors.forename: Pierre
authors.initials: P
authors.lastname: Rahier
authors.forename: Andrée
authors.initials: A
authors.lastname: Houbion
authors.forename: Antoine
authors.initials: A
authors.lastname: Fattaccioli
authors.forename: Mélanie
authors.initials: M
authors.lastname: Gastellier
authors.forename: José
authors.initials: J
authors.lastname: Remacle
authors.forename: Martine
authors.initials: M
authors.lastname: Raes
authors.forename: Patricia
authors.initials: P
authors.lastname: Renard
authors.forename: Thierry
authors.initials: T
authors.lastname: Arnould
mesh_terms: D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020868:Gene Silencing; D005821:Genetic Techniques; D006801:Humans; D007700:Kinetics; D020411:Oligonucleotide Array Sequence Analysis; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism*; D051780:Sterol Regulatory Element Binding Protein 1 / Q000378:metabolism; D013997:Time Factors; D014162:Transfection
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering; C497387:SREBF1 protein, human; D051780:Sterol Regulatory Element Binding Protein 1