De novo DNA methylation induced by siRNA targeted to endogenous transcribed sequences is gene-specific and OsMet1-independent in rice

Small interfering RNA (siRNA) is an essential factor for epigenetic modification of the genome. Recent studies have suggested that endogenous siRNAs induce DNA methylation, chromatin modification and chromatin inactivation at homologous sequences. We have shown that siRNAs targeted to promoter regions of endogenous rice genes induce strong DNA methylation of the targeted sequences, but transcriptional gene silencing is rarely observed. Here, an analysis of epigenetic modifications induced by RNAi targeted to transcribed regions of endogenous rice genes shows that the effects of siRNA are gene-specific, but that they tend to induce higher de novo DNA methylation of CpG dinucleotides than of other cytosines. However, loss of OsMet1 expression by RNAi did not significantly affect levels and patterns of de novo DNA methylation or post-transcriptional mRNA suppression. We also showed that sequence-specific de novo DNA methylation extended both 5' and 3' of the targeted sequences, but there was no significant extension of siRNA signals either 5' or 3'. These results suggest that exogenous siRNAs are strong inducers of de novo DNA methylation in transcribed sequences of rice endogenous genes, but are insufficient to induce heterochromatin formation.