Small interfering RNA (siRNA) targeting of endogenous promoters induces DNA methylation, but not necessarily gene silencing, in rice

Recent evidence indicates that small interfering RNA (siRNA) induces chromatin modifications and inactivation at homologous genomic sequences. A large number of endogenous siRNAs have been discovered that correspond to widely dispersed regions of the genome. We used an experimental system in which transgene-derived siRNAs target promoter regions in rice to determine whether or not siRNAs induce chromatin modifications that result in inactivation. Our results indicate that siRNAs targeted to one transgene and seven endogenous genes induce DNA methylation at all of the target promoters, but do not induce transcriptional suppression. Chromatin immunoprecipitation (ChIP) assays indicate that reduced euchromatic histone modifications were concomitant with the silencing of one endogenous gene, but not of six other endogenous genes that were not silenced. Furthermore, heterchromatic H3K9me2 was higher only in the promoter of the transgene that was completely silenced. These findings lead us to assume that siRNA rarely induces chromatin inactivation or changes in pattern of histone modification, especially H3K9 methylation, within most regions of the genome.