Active DNA Demethylation in Plants

Abstract

Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.

Keywords: 5-methylcytosine; DNA glycosylases; DNA methylation; DNA repair; abiotic stress; base excision; biotic stress; epigenetics; gene imprinting; transposons.

Figure 1

Bipartite DNA glycosylase domain in members of the DEMETER-LIKE (DML) family. (a) Schematic representation of ROS1 domains conserved among DML proteins. (b) Multiple sequence alignment of DML and HhH-GPD representative proteins. Critical residues for catalysis or DNA binding in ROS1 (REPRESSOR OF SILENCING 1) are indicated by asterisks (see text for more details). Names of organisms are abbreviated as follows: Ath, Arabidopsis thaliana; Nta, Nicotiana tabacum; Ta, Triticum aestivum; Osa, Oryza sativa; Zma, Zea mays; Bst, Bacillus stearothermophilus; Eco, Escherichia coli; Mth, Methanobacterium thermoautotrophicum; Mmu, Mus musculus; Hsa, Homo sapiens. Genbank accession numbers are: Ath ROS1: AAP37178; Ath DME: ABC61677; Nta ROS1: BAF52855; Tae DME: AEF38424; Osa DNG701: B8YIE8; Osa ROS1a: XP_015650531; Zma DME1: AQK70999; Bst EndoIII: 1P59; Eco EndoIII: P20625; Mth Mig: NP_039762; Eco MutY: NP_417436; Mmu MBD4: 1NGN; Hsa OGG1: O15527; Eco AlkA: P04395.

Figure 2

Schematic representation of the active DNA demethylation pathway in Arabidopsis. Different 3’ blocked ends are indicated in red. Stimulatory or inhibitory effect of DDB2 over different proteins of active DNA demethylation pathway are indicated with green or red arrows, respectively. See text for details.