title: Introduction of silencing-inducing transgenes does not affect expression of known transcripts.
abstract: While the RNA interference (RNAi) mechanism has only been discovered a decade ago, RNAi is now often used to study gene function by sequence-specific knockdown of gene expression. However, it is still unknown whether introduction of silencing-inducing transgenes alters the transcriptome. To address this question, genome-wide transcriptional changes in silenced and non-silenced backgrounds were monitored through microarray analysis. No significant transcriptional changes were detected when compared to the non-silenced control. This result was confirmed by real-time polymerase chain reaction analysis of genes known to be involved in RNA silencing. In conclusion, introduction of silencing-inducing constructs does not affect expression of known transcripts in other genes than in those homologous to the targeted ones. Consequently, when gene function is studied by RNAi, the transcriptional changes detected will specifically be the result of knockout of the gene of interest, at least for the genes present on the array used in our study.
authors.affiliation: Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.
authors.forename: Thierry
authors.initials: T
authors.lastname: Aelbrecht
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.forename: Melanie
authors.initials: M
authors.lastname: Bauwens
authors.forename: Helena
authors.initials: H
authors.lastname: Van Houdt
authors.forename: Ann
authors.initials: A
authors.lastname: Depicker
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D034741:RNA, Small Interfering