DNA methylation of a 3' cis-element promotes gene activation

In our study, we identified a new transgenerational epigenetic mutant in rice, Epi-LF (Epi-LongFeng). The metastable phenotype of Epi-lf resembles that of rice Epi-d1, and the inheritance is largely similar to that of the agoutiAy mouse mutant. We found that in Epi-lf,mCHH methylation was present in a 155-bp sequence of DNA in close proximity to the 3' end of the LF gene, but the abundance of the siRNAs corresponding to this region was not significantly different from that of the wild type (WT), suggesting that this is a mCHH island like modification. In addition, ectopic mCHH modifications accumulated in the sporophytic tissues and embryos of the Epi-lf mutants. The majority of these ectopic CHH regions did not fit with the OsDRM2 (Domain Rearranged Methylase2)-mediated CHH methylation of genomic regions, suggesting that unknown genetic factors may co-ordinate DNA demethylation and methylation, especially for non-CG methylation. We sequenced transcriptome, methylome and small RNA in different tissues of Eip-lf mutants and wild-type rice