RNA interference-independent reprogramming of DNA methylation in Arabidopsis

DNA methylation is important for silencing transposable elements (TEs) in diverse eukaryotes including plants. In plant genomes, TEs are heavily methylated at cytosines of both CG and non-CG (or CH, where H can be A, T, or C) contexts. The role of RNA interference (RNAi) in establishing TE-specific DNA methylation has been extensively studied, although the significance of RNAi-independent pathways in DNA-methylation reprograming remains unexplored. Here, we directly investigated transgenerational de novo DNA methylation of TEs after the loss of DNA methylation. Our analyses identified very potent and precise RNAi-independent pathways for recovering CH methylation in most TE genes, or coding regions within TEs. Characterization of a small subset of TE genes that did not show CH methylation recovery revealed the impacts of H3K9 demethylation and replacement of histone H2A variants. These chromatin components are conserved between plants and animals and may contribute to chromatin reprograming in a conserved manner. Examination of DNA methylation (WGBS), transcription (RNA-seq), and localization of histone variants (ChIP-seq) in Arabidopsis WT, several DNA methylase and histone modification mutants, and their genetic hybrids.