Abiotic factors

Preceding frequent abiotic stress can acclimatize plants by inducing a change in the epigenetic state, and the persistence of the induced state can be plastic. The epigenetic regulation of the abiotic stress response is complex in nature and could be interlinked with genetic networks or can be an independent event. From literature, we could observe a gap in in-depth studies conducted in natural populations. Most studies are done in artificial environments with model plants or cultivars. Reviews by Bej and Basak (2017) and Li et. al (2017) combined the information on abiotic factors and the contribution of different epigenetic mechanisms for different species (Bej & Basak 2017; Li et al. 2017). ‌In the natural environment, plants are exposed to many abiotic stresses such as salinity, drought, temperature, heavy metals. Epigenetic control of stress-responsive mechanisms was observed in several plant species under various abiotic stress conditions, such as extreme temperatures (Ding et al. 2019), drought (Huang et al. 2019), salinity (Yang and Guo 2018), herbivory, and pathogen (Holeski 2007). For example, increased salinity was associated with DNA methylation changes, histone acetylation, methylation, and phosphorylation in species like rice, Arabidopsis thaliana, tobacco, and mangrove plants (Kim et al. 2015).

In Arabidopsis thaliana, histone modifications are involved in the drought stress response (Kim et al. 2015). For heat stress, DNA methylation differed between heat-sensitive and heat-tolerant genotypes in rapeseed (Gao et al.). And in forest trees (Cork oak), an interplay between DNA methylation and H3 acetylation was observed at elevated temperatures (Correia et al. 2013). Also, cold stress response in A. thaliana and maize affect DNA methylation and histone acetylation (Steward et al. 2002). An interesting example was recently reported by Song et al. (2015), who found that the alpine subnival plant Chorispora bungeana revealed DNA methylation changes that correlated with the exposure to chilling and freezing. Notably, several of the candidate genes were related to physiological chilling and freezing resistance pathways (Song et al. 2015). In summary, induced plant response following abiotic stress seems to be closely related to epigenetic mechanisms that even take an active role in the acclimatization to changing environmental conditions.

Table 1: List of epigenetic modifications reported for abiotic stress:

Components	Stress	Species	Function	References
DNA methylation
ZmMI1	Cold stress	Maize	Stress-induced non-reversible demethylation	Steward et al. 2000
Ac/Ds	Cold stress	Maize	Demethylation of transposon Ac/Ds	Steward et al. 2002
Tam 3	Low temp	Antirrhinum majus	Decrease in methylation	Hashida et al. 2006
NtGPDL	Aluminum, low temp, salt stress	Tobacco	Demethylation at coding region of gene	Choi and Sano 2007
HRS60 and GRS	Salt, osmotic stress	Tobacco	Reversible DNA hypermethylation	Kovarˇik et al. 1997
Histone modifications
AtGCN5	Cold stress	A. thaliana	Affect expression of COR genes	Stockinger et al. 2001 Vlachonasios et al. 2003
Ada2b	Freezing, salt stress	A. thaliana	Induces COR genes	Vlachonasios et al. 2003
SKB1	Salt stress	A. thaliana	Trimethylation of H4K3	Zhang et al. 2011
ABO1/ELO1	Drought stress	A. thaliana	Drought tolerance	Chen et al. 2006
ADH1 and PDC1	Submergence stress	Rice	Histone modifications of H3	Tsuji et al. 2006
HD6	Freezing stress	A. thaliana	Upregulation confer tolerance	To et al. 2011
HOS15	Cold stress	A. thaliana	Deacetylation of histone H4	Zhu et al. 2008
HDA6	Drought stress,cold	A. thaliana	Deacetylation	Kim et al. 2017 Jung et al. 2013
HDA9	Drought and salinity	A. thaliana	Deacetylation	Zheng et al. 2016
HDA15	Drought	A. thaliana	Deacetylation	Lee and Seo 2019)
HDA19	Drought, heat, salinity	A. thaliana	Deacetylation	Ueda et al. 2018a Chen and Wu 2010 Mehdi et al. 2016 Ueda et al. 2017
HDA705	Salinity	Rice	Deacetylation	Zhao et al. 2016
BdHD1	Drought	Brachypodium	Deacetylation	Song et al. 2019
ATX4/5	Drought	A. thaliana	Methyltransferase	Liu et al. 2018)
CAU1/PRMT5/SKB1	Drought and salinity	A. thaliana	Methyltransferase	Fu et al. 2013 Zhang et al. 2011
JMJ15	Salinity	A. thaliana	Demethylase	Shen et al. 2014
JMJ17	Dehydration	A. thaliana	Demethylase	Huang et al. 2019
JMJ15	Salinity	A. thaliana	Demethylase	Shen et al. 2014
JMJ17	Dehydration	A. thaliana	Demethylase	Huang et al. 2019
Small RNA
miR398	oxidative stress-causing agents such as high light levels, Cu2+, Fe3+ and methyl viologen	A. thaliana	posttranscriptional CSD1 and CSD2 mRNA accumulation and oxidative stress tolerance	Sunkar et al. 2007
miR393	Cold, dehydration, NaCl, and ABA stress	A. thaliana	miR393 is strongly upregulated by mentioned treatments	Sunkar and Zhu 2004