Table 2.

Plant responses to stress and epigenetic processes in different plant species.

Plant Response	Epigenetic Process	Plant Species	Function	Reference
Heat stress	Histone modification	Arabidopsis thaliana	HDA9 interacts with the PWR protein and increases H3K9 deacetylation at the +1 nucleosomes of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and YUCCA8 (YUC8), essential genes regulating thermomorphogenesis.	[85]
			HDA9 promotes the eviction of the histone variant H2A.Z from the YUC8 nucleosome and enables its transcriptional activation by PIF4, mediating the thermomorphogenic response.	[86]
			HDA15 acts as a repressor of warm-temperature marker genes (YUCCA8, IAA19, IAA29, TCH3, ATHB2, and XTR7) under normal conditions but dissociates from its targets under elevated-temperature stimuli, inducing their expressions.	[88]
	DNA methylation	Brassica napus	Exhibits more DNA demethylation events in heat-tolerant genotypes, which are associated with heat-stress response and adaptation.	[80]
Drought stress	DNA methylation/histone modification	Populus deltoides × P. nigra	Shows genotypic variation in DNA hypomethylation that correlates with morphological traits related to productivity under drought stress. Histone acetylation induces rapid gene expression associated with heat-shock proteins (HSPs) under drought-stress conditions.	[93]
	Histone modification	Arabidopsis thaliana	HDA9 negatively regulates plant sensitivity to drought stresses through increased H3K9ac levels in the promoter region of 14 drought-response genes under water-deficit conditions.	[92]
			AtHD2C physically interacts with HDA6 and regulates the expressions of ABA-responsive genes in association.	[97,98]
		Brachypodium distachyon	Exhibits increased expressions of five HAT genes (BdHAG1, BdHAG3, BdHAC1, BdHAC4, BdHAF1) under drought treatment, playing a role in drought-stress response and adaptation.	[95]
		Brassica rapa	Demonstrates a significant increase in the expressions of nine HAT genes (BraHAC1, BraHAC2, BraHAC3, BraHAC4, BraHAC7, BraHAG2, BraHAG5, BraHAG7, and BraHAF1) after drought treatment, contributing to drought-stress response and adaptation.	[94]
		Gossypium hirsutum	Enhanced drought tolerance by reducing H3K9ac levels in the promoter region of GhWRKY33, a negative regulator of drought response, through the action of GhHDT4D, a member of the histone deacetylase HD2 subfamily.	[81]
		Dendrobium officinale	Induces the expressions of DoHDA10 and DoHDT4 genes in roots, stems, and leaves under drought-stress conditions.	[107]
		Oryza sativa	Triggers the expressions of nine HAT (OsHAG702//703, OsHAD704/705/706/711/712/713, and OsHAM701) genes under drought conditions. Some HAT genes contain drought-sensitive elements, such as the MBS cis element, in their promoter regions.	[90]
		Triticum aestivum	Demonstrates the downregulation of five HDA genes and a significant increase in TaHAC2 expression in the drought-resistant variety BL207 under drought-stress conditions.	[91]