Fig 1

Representation of gene and transposon loci in wild-type, met1, and epihybrid plants. a Some genic regions in wild-type (Col-0) plants exhibit CG methylation (red) and have moderate expression levels, in part mediated by continual removal of H3K9me2 by IBM1 (purple circles). Transposons in wild-type plants are highly decorated with CG, CHG (blue), and CHH (black) methylation; they have no interaction with functional IBM1 and are not expressed. b In the met1 mutant, some genic regions exhibit low levels of CHG and CHH methylation as a result of depleted IBM1, which is itself sensitive to loss of CG methylation. In met1, certain transposons are moderately expressed and have intermediate CHG and CHH methylation levels. c The Col-0-derived genic regions of epihybrid plants exhibit near wild-type levels of CG methylation on the wild-type allele (yellow), but might additionally contain limited CHG and CHH methylation (represented by the ‘?’). By contrast, the met1-derived allele does not newly acquire CG methylation. In epihybrid plants, unlike in wild-type plants, IBM1 is not entirely localized to Col-0-derived genic regions. Instead, transcriptional reactivation of certain transposons occurs in the epihybrids, which probably depletes IBM1 in genic regions and relocates it to transposons. The net effect is that these transcriptionally active transposons have reduced CHG methylation. The length of the arrow within each allele indicates transcription strength.