The DME demethylase regulates sporophyte gene expression, cell proliferation, differentitation and meristem resurrection

The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In Arabidopsis, genome-wide DNA demethylation is required for normal gamete development, catalyzed by the DEMETER (DME) DNA demethylase, specifically in the companion cells of male and female gametophyte, respectively. In the sporophyte, post-embryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Previously, we demonstrated that DME is expressed in meristems and actively dividing tissues during sporophytic development, although its function in the sporophyte has remained elusive. Here, we show that sporophytic DME activity exerts a profound effect on the transcriptome of the developing plant. Comparative analyses of related epigenetic regulators reveal that, in some cases, transcriptional differences in dme mutant sporophytic tissues are likely linked to a loss of DME-mediated DNA demethylation. We also identify numerous phenotypic traits in dme-2 sporophytic mutants, including delayed seed germination, root and root hair development, aberrant cellular proliferation and de-differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence cell and stomatal precursor cells, and inflorescence meristem resurrection. Further, we identify strong links between dme-2 sporophytic phenotypes and the dysregulated gene expression pathways observed. Our results demonstrate that DME is required for normal sporophytic development, and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activity during the sporophytic life cycle in Arabidopsis.