DNA Methylation

María Estefanía López

Summary

DNA methylation plays a crucial role in the regulation of gene expression, in the activity of transposable elements, in the defense against foreign DNA, and even in the inheritance of specific gene expression patterns (Xu, Tanino, & Robinson, 2016; Finnegan, Genger, Peacock, & Dennis, 1998; Xu, Tanino, Horner, & Robinson, 2016). DNA methylation refers to the cytosine methylation process through the covalent enzyme-catalyzed transfer of a methyl group from S-adenosylmethionine to the 5’ position of cytosine, thus converting cytosine to 5-methylcytosine (5mC) (Pikaard et al., 2014; Sahu et al., 2013). DNA methylation in plants is species-, tissue-, organelle-, and age-specific. It is controlled by phytohormones, changes during plant development, and biotic and abiotic stress conditions (Finnegan et al., 1998). This epigenetic mark can be accumulated during plant vegetative phases and, principally, be passed on to the next generations. DNA cytosine methylation appears in three contexts, CG, CHG, and CHH, where H can be A, C, or T (Sahu et al., 2013). It predominantly occurs on transposons and other repetitive DNA elements in the genome. DNA methylation patterns must be stably maintained to ensure that transposons remain silenced and preserve cell-type identity. Three different pathways maintain DNA methylation differing in their central enzyme: the DNA METHYLTRANSFERASE 1 (MET1) maintains CG methylation, the CHROMOMETHYLASE (CMT3), a plant-specific DNA methyltransferase, maintains CHG methylation, and the DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) maintains the asymmetric CHH methylation through de novo methylation (Law & Jacobsen, 2011). Although DNA methylation is a stable epigenetic mark in most cases, reduced levels of methylation are observed during plant development. Methylation loss can either occur passively via replication without functional maintenance methylation pathways or actively by removing methylated cytosines with DNA glycosylase activity. The symmetrical CG or CHG methylation is inherited during the DNA replication in the form of hemimethylated sequences. It provides the memory of the methylation imprint present in the parental DNA, suggesting a role in stress protection memory (Suzuki & Bird, 2008). On the contrary, the asymmetrical cytosine methylation must be reestablished de novo after each replication cycle. DNA methylation in plants is closely associated with histone modifications, and it affects the binding of specific proteins to DNA and the formation of respective transcription complexes in the chromatin (Pikaard et al., 2014; Zamir, 2001). Those epigenetic marks trigger chromatin remodeling, which plays a crucial role not only in transcriptional regulation but also in DNA repair and replication (Kim et al., 2019). It has been proposed that MET1 and DDM1 could be involved in the DNA damage response reducing chromatin density (Kim et al., 2019; Shaked, Avivi-ragolsky, & Levy, 2006). DDM1 mutations generate a strong alteration in the nuclear organization and chromatin structure, particularly in the centromeric and pericentromeric regions, resulting in the impediment of the DNA repair machinery that loses its access to the damaged sequences. This emphasizes the broad involvement of recombination and DNA repair proteins in plant genome maintenance and the link between epigenetic and genetic processes.

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