DNA methylation is the primary epigenetic mark

DNA methylation through the years has become an evolutionary preserved mechanism that has contributed to the divergence of prokaryotes and eukaryotes, helping them adapt to different environmental conditions over the years (Bewick & Schmitz, 2017). Epigenetic modifications, including DNA methylation, histone modifications, and the expression of non-coding RNAs (ncRNA), influence the chromatin structure and alter the accessibility of genomic regions for interacting enzymes (H. Zhang, Lang, & Zhu, 2018). This means that DNA methylation is essential to many biological processes directly modifying the genome architecture, the definition of Euchromatin and Heterochromatin, and the control of gene expression (Bewick & Schmitz, 2017; H. Zhang et al., 2018). Dysfunctions of DNA methylation can lead to abnormalities in plants, such as failure in tomato and orange fruit ripening or vice versa promote early strawberry fruit ripening (Cheng et al., 2018; Huang et al., 2019; H. Zhang et al., 2018).

The genomic location of DNA methylation can display different roles in the maintenance of the structure and integrity of the genome and gene expression regulation (Bewick & Schmitz, 2017). In combination with histone modifications and other interacting proteins, DNA methylation defines the chromatin structure and, through this, the accessibility of the DNA. DNA methylation helps to regulate gene expression, transposon silencing, chromosome interactions (Fig. 1) (Zhang et al., 2018). To Illustrate, in plants, DNA methylation is distributed at the body of genes (where the function is often unclear) and at repetitive regions, where it restricts the expression of TEs, which represent in some plant species more than 80% of the genome, e.g., barley, sunflower, and maize. (Meyer, 2011; Vitte, Fustier, Alix, & Tenaillon, 2014). The function of the variability of DNA methylation in some genomic regions in some plant species remains a mystery (Zilberman, 2017). For example, five different apple cultivars showed differential methylation patterns in promoter regions of genes that regulate the anthocyanin pathway. Even though changes in the transcription of these genes generate different red-skin phenotypes, methylation was not the main factor to alter their expression (Jiang et al., 2019).

In plants, methylation can occur in distinct site classes based on the sequence context with which the methylated cytosine (mC) is accompanied. There are three sequence contexts, including the dinucleotide CpG or CG sites (mCG, the p marks the phosphate), and the trinucleotides CHG and CHH (mCHG and mCHH), where H can be adenine (A), cytosine (C), or thiamine (T) (Bewick & Schmitz, 2017). This contrasts with mammals, where methylation is primarily found in the CG context and, in specific cell types, also in the CH context (Chad E. & Schmitz, 2017).

The most common type of methylation across the different kingdoms, CG methylation, is also the most predominant in plants (Chad E. & Schmitz, 2017). One reason for this wide distribution is probably found in the relatively simple maintenance mechanism after DNA replication. Because CG and CHG contexts are symmetrical, due to the obligatory cytosine on the complementary strand (i.e., complementary to G), cytosine methylation can be copied from the old strand to the newly synthesized strand. In comparison, CHH sites are asymmetrical (i.e., the complementary strand does not contain C) and require special machinery to be maintained during DNA replication since no complementary methylated sequence is available to guide the re-methylation (Foyer & Noctor, 2013). In summary, cytosine methylation is the primary epigenetic mark, partly because it is technically easy to access (see Chapter 11). However, the consequences of cytosine methylation at a specific site depend on the position and the sequence context and are not easily interpreted.