Genome-Wide Demethylation of <i>Arabidopsis</i> Endosperm

TLDR

In Arabidopsis thaliana endosperm, imprinted gene expression is regulated by maternal genome demethylation mediated by DEMETER, but the full extent of these changes was previously unknown. We show that nearly the entire endosperm genome is demethylated, with local non‑CG hypermethylation of siRNA‑targeted sequences, embryo‑specific CHH hypermethylation of transposons, and that DEMETER loss partially restores CG methylation, indicating a reconfigured methylation landscape that likely reinforces transposon silencing in the embryo.

Abstract

Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA-targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.