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.

Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture

“…Finally, it should be emphasized that the moderated mediation model presented in this study failed to explain the demethylation of CG sites, although the reason for this result is not apparent. However, we interpret the results in terms of how the process of DNA demethylation and its maintenance differ between the two sequence contexts [7,92]. Epigenetic mechanisms involved in demethylation of the CHG context [93] or maintenance of methylation [94] are most likely crucial here.…”

Reactive Oxygen Species (ROS) and Nucleic Acid Modifications during Seed Dormancy

“…Passive demethylation is due to subsequent rounds of DNA replication without the maintenance of the methylation pattern. Active demethylation is catalysed by DNA glycosylases -DEMETER (DME), REPRESSOR OF SILENCING1/DEMETER-LIKE 1 (ROS1), DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3), in A. thaliana [89].…”

“…Recent studies have shown the importance of genomic imprinting, through DNA-methylation, in regulating the expression in the endosperm of two maternally expressed negative regulators of seed dormancy, DOG1-LIKE 4 (DOGL4) and ALLANTOINASE (ALN) [106,107]. In A. thaliana, active DNA demethylation depends on the activity of ROS1, which directly excises methyl-C from DNA [89]. Interestingly, ros1 mutants are hypersensitive to ABA during early seedling development [108], showing that ROS1-driven DNA demethylation regulates seed dormancy, and the response to ABA by controlling the expression of DOGL4, a negative regulator of seed dormancy and the ABA response.…”

Genome editing for plant research and crop improvement

“…The use of TET1 for demethylation generates stable 5‐methylcytosine (5‐meC) derivatives which could be independent epigenetic marks on their own and/or have unknown regulatory roles. Plants can follow a different path of active demethylation by directly removing 5‐meC using DNA glycosylases/lyases (Parrilla‐Doblas et al, 2019). The DNA glycosylase activity of the Arabidopsis REPRESOR OF SILENCING 1 (ROS1) can remove 5‐methylcytosine from the DNA backbone before its lyase activity cleaves the DNA backbone at the site of 5‐methylcytosine removal (Agius et al, 2006; Zhu et al, 2007).…”