The 5-methylcytosine DNA glycosylase ROS1 prevents paternal genome hypermethylation in Arabidopsis endosperm

DNA methylation patterning is a consequence of opposing activities of DNA methyltransferases and DNA demethylases. In many plant and animal species, reproduction is a period of significant epigenome lability. In flowering plants, two distinct female gametes, the egg cell and the central cell, are fertilized to produce the embryo and the endosperm of the seed. The endosperm is an unusual tissue, exemplified by triploidy and reduced DNA methylation. In Arabidopsis thaliana, a 5-methylcytosine DNA glycosylase, DME, demethylates regions of the central cell genome, leading to methylation differences between maternally- and paternally-inherited endosperm genomes after fertilization. Expression of DME in the central cell is required for gene imprinting, or parent-of-origin specific gene expression, in endosperm. DME is part of a four member gene family in Arabidopsis that includes ROS1, DML2, and DML3. It is unknown whether any of the other DNA glycosylases are required for endosperm methylation patterning.

Using whole-genome methylation profiling, we identify ROS1 target regions in the endosperm. We show that ROS1 prevents hypermethylation of paternally-inherited alleles in the endosperm at regions that lack maternal or paternal allele methylation in wild-type endosperm. Additionally, we demonstrate that at many ROS1 target regions the maternal alleles are demethylated by DME.

ROS1 promotes epigenetic symmetry between parental genomes in the endosperm by preventing CG methylation gain on the paternal genome. We conclude that ROS1 and DME act in a parent-of-origin-specific manner at shared endosperm targets, and consider possible implications for the evolution of imprinting mechanisms.