The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis

Abstract

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, but how it is recruited to these differing chromatin landscapes is unknown. The C-terminal half of DME consists of 3 conserved regions required for catalysis in vitro. We show that this catalytic core guides active demethylation at endogenous targets, rescuing dme developmental and genomic hypermethylation phenotypes. However, without the N terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. Comparative analysis revealed that the conserved DME N-terminal domains are present only in flowering plants, whereas the domain architecture of DME-like proteins in nonvascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance

“…In the vegetative nucleus of the pollen, DME is required for pollen germination and for the growth of the pollen tube. A complementation line expressing a DME native promoter-driven DME catalytic domain sequence rescued the dme-2 pollen defects (Zhang et al, 2019). Surprisingly, central cell-specific complementation lines in the current study did not show a seed-abortion phenotype, even though the lines had a strong mutant allele background.…”

“…It appears that DME is required for both PTI and ETI. Mutants of the DNA methyltransferase and RNA‐directed DNA methylation pathways showed a decreased susceptibility to pathogen attack (Dowen et al, 2012; Zhang and Zhu, 2012; Deleris et al, 2016; López Sánchez et al, 2016); thus, these pathways play antagonistic roles in disease resistance (López Sánchez et al, 2016). DME may prevent the transcriptional silencing of genes important for these defense responses (Figure S9).…”

“…DNA methylation at cytosine residues is an important and conserved epigenetic modification in many eukaryotes, including plants, and is associated with the suppression of transposable elements (TEs) and the regulation of gene expression (Zhu, 2009; Zhang and Zhu, 2012; Zhang et al, 2018; Liu and Lang, 2020). In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (H represents A, T, or C).…”

Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

“…For DNA demethylase, ROS1 dysfunction can silence the expression of the RD29A gene, because of its hypermethylation at the RD29A promoter [ 50 ]. DME activates maternal FIS2 , FWA , and MEA allele expression, and is responsible for endosperm gene imprinting and seed viability [ 51 ]. SlDML2 , a ROS1 ortholog, is required for tomato fruit ripening, by activating DNA demethylation and promoting the expression of fruit-ripening genes, such as CNR , PSY1 , and RIN [ 13 ].…”

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

“…In this case, only the old (maternal) chain appears to be methylated [ 26 ]. In contrast, active demethylation relies on the activity of demethylases represented in Arabidopsis by four enzymes: DEMETER (DME), REPRESSOR OR SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DEMETER-LIKE 3 (DML3) [ 167 , 168 ].…”