Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons

Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/ absent methylation patterns. However, we show here that, in Arabidopsis thaliana h1ddm1 mutants, interme-diate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably in-herited at any level via a dynamic balance of these activities. We find that DRM2-the core methyltransferase of the RNA-directed DNA methylation pathway-catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.

Automated summary

In Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG can be stably inherited across many generations and is quantitatively associated with transposon expression. A mathematical model estimates that mCG can be stably inherited at any level via a dynamic balance of semiconservative maintenance failure and de novo methylation. The core methyltransferase DRM2 catalyzes most of the heterochromatic de novo mCG, with much higher rates than previously thought, while chromomethylases make smaller contributions. These results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.