Gene silencing through transcriptional repression can be induced by double-stranded RNA (dsRNA) that targets a gene promoter. This phenomenon, termed RNA-mediated transcriptional gene silencing (TGS), was first discovered in plants using a transgene that transcribes an inverted repeat of promoter sequence. However, endogenous genes differ from transgenes in the feasibility of TGS induction, by being more resistant to silencing. Heritable, transgenerational silencing of an endogenous gene has been induced by targeting dsRNA to the promoter in petunia and tomato plants, using a vector based on Cucumber mosaic virus. Efficient TGS depends on the function of a viral protein, which can facilitate epigenetic modifications through the transport of short interfering RNA to the nucleus. The efficiency of the TGS also depends on the length and nucleotide composition of the promoter RNA segments. Such epigenetic changes induced by the viral vector results in a novel class of modified plant, a plant that does not carry a transgene but has altered traits. Thus, TGS to modify the epigenetic state of a plant is now a feasible tool to engineer novel traits. Here we review epigenetic changes induced in a particular gene through RNA-directed DNA methylation and those induced randomly on the genome in terms of their use for plant biotechnology.