Gene silencing and modeling of gene expression are classical approaches in studying gene functions. There are many methods available which use RNA molecules as gene silencing inducers or gene expression modulators. RNA molecules act at different levels of gene expression: chromatin structure, gene transcription and pre-mRNA maturation. In the last decade, new methods for silencing and modeling of gene expression emerged, utilizing RNAi phenomenon, trans-splicing, RNA directed DNA metylation, ribozymes, artificial microRNAs, ryboswitches, and U1 interference. In this paper, we review some of the methods which were successfully used for gene function studies and as therapeutic tools against different plant and human diseases.