By preventing or suppressing transcription, DNA methylation modifies gene expression in response to abiotic stresses. DNA methylation pattern greatly influenced the way through which plants respond to the abiotic stresses (Boyko and Kovalchuk 2008). Environmental stimuli lead to changes in extent of DNA methylation either upward in case of hypermethylation and downward in hypomethylation and consequent changes in degree of DNA methylation also depends upon the type of stress response prevalent (Bonasio et al. 2010). Under saline conditions hypermethylation was reported in mangrove and rice plants (Karan et al. 2012). While drought-tolerant rice genotypes were hypomethylated, rice genotypes cultivated under drought conditions tended to be hypermethylated (Gayacharan and Joel 2013).
The methylation of CNN, CNG, and CG by DRM2 and CMT3 also plays a role in stress. In rice, CG methylation is found primarily in genic regions, whereas non-CG methylation (CHH and CHG) is mostly found in TEs (Zemach et al. 2010). As a result, tobacco plants exposed to cold and salt stress in the presence of paraquat and aluminium have shown CG demethylation in the coding area of the NtGPDL (glycerophosphodiesterase-like protein) gene (Choi and Sano 2007). Hypermethylation of CG and CHG islands of pea genome and satellite DNA of halophytes respectively due to osmotic stress leads to shift in C3 pathway to CAM (crassulacean acid metabolism) (Dyachenko et al. 2006). Moreover, after withdrawal of stress, hypermethylation revert back to original state. In this context Kovarik et al. (1997) delineated CHG hypermethylation under the saline and osmotic stress of tobacco suspension culture and subsequently reversion occurs under the normal conditions. In contrast to it, demethylation not revert back when chilling stress removed in maize (Steward et al. 2002). There are several different ways that methylation and demethylation at genic or non-genic regions might affect the transcript that is produced. It has been demonstrated that methylating the gene's flanking sequence, 3′ region, and promoter suppresses gene expression. Methylation in the promoter region is associated with gene downregulation, but methylation in the genic region has a parabolic connection with transcription. Genes with the lowest expression levels have the highest likelihood of methylation, while genes with the highest expression levels have the lowest likelihood (Zemach et al. 2010; Zilberman et al. 2007). Transposable elements' distinctive methylation patterns contribute to the way that plants acquire different adaptations (Cantu et al. 2010). A retrotransposon-like sequence (ZmMI1) revealed demethylation patterns in maize roots under cold stress (Steward et al. 2000). Severe cold stress in Antirrhinum majus reduced methylation status and elevated the excision rate of a specific transposon, Tam3 (Hashida et al. 2006). Stress-mediated induction of transposons have been observed for Tos17 (rice) (Hirochika et al. 1996), Tnt1 (tobacco) (Beguiristain et al. 2001), and BARE-1 (barley) (Kalendar et al. 2000). Recent research has also revealed that some retrotransposons (ONSEN, an LTR-copia type retrotransposon in Arabidopsis) use demethylation to activate themselves under heat stress (Cavrak et al. 2014). Histone alterations are important in both plant growth and stress responses. While histone tail phosphorylation, ubiquitination and acetylation, are related with gene up-regulation, de-acetylation and biotinylation are connected with down-regulation of genes (Chen et al. 2010). In response to abiotic stresses, plants experience a variety of dynamic alterations to histone tails. Tobacco plant cells subjected to salt stress, cold, and abscisic acid (ABA) phosphorylated, phospho-acetylated, and acetylated H3 Ser10, H3 Ser10, and H4 lys14, respectively (Sokol et al. 2007). This histone modification causes an upregulation of stress-related genes. Increased acetylation of H3K9 and H3K4 in the coding areas of dehydration sensitive genes i.e., Rd29A, RD29B, RD20, and RAP2.4 of Arabidopsis results in their upregulation (Kim J et al. 2009). In Arabidopsis and wheat, UV-B exposure increased acetylation of H3K9/K14 in the promoter area of ELIP1 (Cloix and Jenkins 2008). Chen et al. (2010) also discovered that ABA induced and salt stress-induced gene activation is related with the elevation of marks such as H3K9/K14ac and H3K4me3, as well as the reduction of gene repression marks such as H3K9me2 at ABA and other abiotic stress-responsive genes. The offsprings of stressed plants displayed hypermethylation after being exposed to varied levels of salt stress in Arabidopsis plants (Boyko et al. 2010). Chen et al. (2010) also discovered that salt stress and ABA induced gene expression is connected with the elevation of gene activation marks such as H3K9/K14ac and H3K4me3, as well as the reduction of H3K9me2.
The accumulation of multiple new antisense transcripts, a source of siRNAs, induced by abiotic stressors highlights the importance of these transcripts against stress (Zeller et al. 2009). Hc-siRNAs, siR441 and siR446 were discovered to be downregulated in response to abiotic challenges but show a surge in the synthesis of their precursors, signalling that the processing of siRNA precursors is hindered, which seems to be a stress responsive mechanism (Yan et al. 2011).
Furthermore, nat-siRNAs (Natural antisense short interfering RNA) and ta-siRNAs (Trans-acting siRNA) have been known to have direct implications against stress response. Under salt stress, Arabidopsis forms nat-siRNAs by double stranded overlapping antisense transcription of the gene P5CDH (DELTA1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE), which results in buildup of proline in cell (Borsani et al. 2005). One crucial metabolite thought to be involved in salt tolerance is proline. Plant development is regulated by the presence of Ta-siRNAs in stressful conditions (Schwab et al. 2009). Furthermore, siRNA can affect one-third of the methylation of chromosomal sites since they are associated with RdDM (Lister et al. 2008). SlAGO4, a substantial orthologue of AGO4 (the main factor of RdDM), performs a crucial role in tomato under drought and salt stress. (Huang et al. 2016). RdDM is crucial to the tobacco plant's defense against geminivirus infection, according to iTRAQ study on the plant (Zhong et al. 2017). Twenty six new miRNAs that were either up- or down-regulated by abiotic stresses were discovered in a study of Arabidopsis seedlings (Sunkar and Zhu 2004). Cold stress was discovered to downregulate miR319 in rice (Lv et al. 2010), but multiple families of miRNAs were found to be over expressed in Brachypodium (Zhang et al. 2009). MiR396 overexpression in rice and Arabidopsis plants improved tolerance to salt and alkaline stress (Gao et al. 2010). In these plants that respond to stress tolerance, these variations in miRNA concentration are associated with an important modulation of miRNA targets. Table 1 lists reports that epigenetic mechanisms, such as DNA methylation, histone modification, and RNA-directed DNA methylation, can protect plants from a variety of abiotic stresses.
In cold-climate adapted plant species, vernalization is a well-known process that suppresses flowering during vegetative growth in winter and, under favourable circumstances in spring, enable flowering during the reproductive phase (Kim DH et al. 2009). FLOWERING LOCUS C (FLC) is a well-studied regulatory locus in Arabidopsis that regulates flowering period epigenetically (Whittaker and Dean 2017). Additionally, FLC prevents Arabidopsis from blossoming in cold climate (Bastow et al. 2004). In this context, Polycomb-mediated epigenetic regulation, which involves lncRNAs in lowering FLC locus expression through vernalization mechanism, is a well-established technique for altering cold acclimation in Arabidopsis. As a result of chromatin alteration at the FLC locus during vernalization (decreasing active histone mark H3K36me3 and augmenting repressive histone mark H3K27me3), COLD INDUCED LONG ANTISENSE INTRAGENIC RNAs (COOLAIR), an alternatively spliced NAT lncRNA, are responsible for FLC locus repression (Csorba et al. 2014). It has been discovered that in the species Arabidopsis thaliana, Arabidopsis alpina, and Arabidopsis lyrata, the class I antisense COOLAIR regulates FLC repression during vernalization (Castaings et al. 2014). Similar to this, the FLC gene intron1-coded COLD ASSISTED INTRONIC NONCODING RNA (COLDAIR) (Heo and Sung 2011) draws the Polycomb Repressive Complex 2 (PRC2), which assists in FLC locus chromatin modification (increase H3K27me3) and represses FLC locus expression (Fig. 1). After that, Kim DH et al. (2009) suggested that "Polycomb-binding lncRNA, COLDWRAP" may be involved in the ongoing control of the FLC gene in Arabidopsis during vernalization.
To adapt to climate change and the rise in unexpected climatic conditions, plants have developed genetic and epigenetic systems that enable them to bear single or combination stresses and their interactions (Shanker and Venkateswarlu, 2011). Knowing the genetic and epigenetic underpinnings of these reactions is therefore necessary in order to comprehend the complexity of crop responses to environmental alterations. In order to identify genes that are specifically required for heat stress memory but not for the initial reactions to heat, Brzezinka et al. in 2016 employed heat stress priming model to delineate the memory of abiotic stresses in Arabidopsis. In order to ensure that the heat-inducible genes are always accessible and active, it has been found that the FORGETTER1 (FGT1) gene produces the FGT1 protein, which binds directly to a specific class of heat-inducible genes. This is accomplished by changing the way the DNA containing these genes is packed. Because it is crucial for breeding applications to comprehend the stability and heredity of epigenetic marks and epigenetic regulatory systems, their discoveries may result in fresh strategies for crop breeding programmes to increase resilience to abiotic stress (Gallusci et al., 2017). A few crop-related cases were covered in more detail in this chapter (Table 1).