Inverted-Repeat RNAs Targeting FT Intronic Regions Promote FT Expression in Arabidopsis

Transcriptional gene silencing (TGS) is often associated with promoter methylation in both animals and plants. However, the function of DNA methylation in the intragenic region remains unclear. Here, we confirmed that promoter methylation of FLOWERING LOCUS T (FT) led to gene silencing; in contrast, we found that intragenic methylation triggered by RNA-directed DNA methylation (RdDM) promoted FT expression. DNA methylation of the FT gene body blocked FLC repressor binding to the CArG boxes. However, when the boxes were not directly targeted by inverted-repeat RNAs (IRs), FLC binding blocked spreading of DNA methylation to theses sequences. Notwithstanding the FLC binding, FT was still activated under this condition. The DNA methylation was accompanied by elevated H3K9 methylation levels on the FT gene body. More importantly, the FT diurnal and organ-specific expression pattern was preserved in the activated plants. Our data demonstrate that the same type of epigenetic modification can lead to an opposite genetic outcome depending on the location of the modification on the gene locus. Moreover, we highlight a novel strategy to activate gene expression without changing its spatio-temporal regulatory patterns.