The stability of epigenetic patterns is critical for genome integrity and gene expression. This highly coordinated process involves interrelated positive and negative regulators that impact distinct epigenetic marks, including DNA methylation and dimethylation at histone H3 lysine 9 (H3K9me2). In Arabidopsis, mutations in the DNA methyltransferase MET1, which maintains CG methylation, result in aberrant patterns of other epigenetic marks, including ectopic non-CG methylation and the relocation of H3K9me2 from heterochromatin into generich chromosome regions. Here, we show that the expression of the H3K9 demethylase IBM1 (increase in BONSAI methylation 1) requires DNA methylation. Surprisingly, the regulatory methylated region is contained in an unusually large intron that is conserved in IBM1 orthologues. The re-establishment of IBM1 expression in met1 mutants restored the wild-type H3K9me2 nuclear patterns, non-CG DNA methylation and transcriptional patterns at selected loci, which included DNA demethylase genes. These results provide a mechanistic explanation for long-standing puzzling observations in met1 mutants and reveal yet another layer of control in the interplay between DNA methylation and histone modification, which stabilizes DNA methylation patterns at genes.

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.DNA methylation | transcription | transposable elements | gene silencing | Arabidopsis I n eukaryotic genomes, cytosine methylation represents an epigenetic mark involved in the silencing of transposable elements (TEs), genes, and transgenes (1, 2). In plant genomes, TEs are typically silent and associated with dense DNA methylation in the three cytosine contexts CG, CHG, and CHH (where H is any base but G). Repression of gene transcription by DNA methylation often correlates with methylation of promoter sequences whereas transcriptionally active protein-coding genes tend to be methylated exclusively at CG positions in their bodies (3)(4)(5)(6).In the plant Arabidopsis thaliana (Arabidopsis), faithful propagation of CG methylation patterns upon de novo DNA synthesis during DNA replication is safeguarded by the DNA methyltransferase METHYLTRANSFERASE 1 (MET1), the plant homolog of human DNA methyltransferase 1, such that symmetrical CG sites in the genome are usually either fully methylated or not at all (7,8). Maintenance of non-CG methylation is more complex and involves the partially redundant activities of the DNA methyltransferases DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), CHROMOMETHYLASE 2 (CMT2), and CHROMOMETHYLASE 3 (CMT3). The three proteins act in self-reinforcing methylation and silencing loops that also rely on histone H3 methylation at lysine 9 (H3K9me) and small RNAs of 24 nt in length (9-12). The interplay between chromatin and methylation is also apparent from the activity of the DECREASE IN DNA METHYLATION 1 (DDM1) chromatin remodeler, which seems to control access of methyltransferases to their H1-containing heterochromatic DNA targets (10).Similar to changes in DNA sequence, differences in DNA methylation, either of natural, spontaneous origin or experimentally induced, can impact genome stability, gene expression, and phenotypic variation. Deficiencies in DDM1 induce drastic hypomethylation of heterochromatin at all cytosine contexts, resulting in tran...