DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana

Abstract

Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.

Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis

“…The response to spaceflight includes differential DNA methylation in a manner that is similar to known terrestrial stress responses, particularly those associated with pathogen attack or harsh environments. Supplementary Table 2 provides a comparison of these spaceflight-associated DmC-DEGs with those from several terrestrial studies of environmental stress responses ( Yong-Villalobos et al, 2016 ; Hewezi et al, 2017 , 2018 ; Stassen et al, 2018 ; Korotko et al, 2021 ). This correlation strongly suggests that the spaceflight response, though novel, utilizes a range of mechanistic approaches that are typically employed during terrestrial environmental stress.…”

“…DNA methylation profiles within a genome are dynamic and complex, yet integral to plant growth, development, and stress responses (reviewed in: Bartels et al, 2018 ). Many terrestrial abiotic stresses, such as salt stress, heat stress, drought, water stress, and phosphate starvation induce epigenetic changes that aid in the adaptation process (e.g., Labra et al, 2002 ; Boyko and Kovalchuk, 2010 ; Mirouze and Paszkowski, 2011 ; Bilichak et al, 2012 ; Colaneri and Jones, 2013 ; Tricker et al, 2013 ; Yong-Villalobos et al, 2015 , 2016 ; Hewezi et al, 2017 , 2018 ; Bartels et al, 2018 ; Kenchanmane Raju et al, 2018 ; Beyrne et al, 2019 ; Ashapkin et al, 2020 ; Akhter et al, 2021 ; Korotko et al, 2021 ; Laanen et al, 2021 ; Villagomez-Aranda et al, 2021 ). The genes differentially expressed in response to spaceflight share similarities with many documented terrestrial responses.…”

Heat Stress in Pinus halepensis Somatic Embryogenesis Induction: Effect in DNA Methylation and Differential Expression of Stress-Related Genes

“…On the contrary, in Norway spruce, seedlings originating from a warm embryonic environment [43] and the exposure of Arabidopsis plants to heat [44] resulted in an increase of global DNA methylation. Interestingly, also in Arabidopsis, DNA methylation increased during heat stress, followed by the reduction of DNA methylation levels after transfer to the control conditions [36].…”

“…One of the most important epigenetic marks is DNA methylation. It occurs through the addition of a methyl group at position 5 of the pyrimidine ring of cytosine in the CG, CHG, and CHH (where H = A, T, or C) contexts [34,35], and understanding how its levels change under stressful conditions can lead to a better knowledge of the plant response to environmental changes [11,36]. Considering the use of epigenetic variations for breeding applications relies on their transmission features, and since 5mC patterns can be transmitted through mitosis as well as meiosis, this DNA methylation mark could be valuable in all crops regardless of their propagation method [37].…”

The Epigenetic Mechanisms Underlying Thermomorphogenesis and Heat Stress Responses in Arabidopsis

“…Epigenetic changes also take place during the recovery period from HS, to facilitate a plant to develop a HS memory. Differentially methylated cytosine (DMC) analysis in Arabidopsis under HS, HS recovery, and control temperature conditions, depicted that DNA methylation increased during HS and decreased during the recovery period [57]. Additionally, histone H3K4 methylation negatively affects the RdDM pathway and results in hypomethylation [58].…”