Fact sheet 1: DNA Methylation

María-Estefanía López

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 cytosine methylation process through the covalent enzyme-catalyzed transfer of methyl group from S-adenosylmethionine to 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 under biotic and abiotic stress conditions (Finnegan et al., 1998). This epigenetic mark can be accumulated during plant vegetative phases and be passed on to the next generations by germline cells. 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 in order to ensure that transposons remain in a silenced state and to preserve cell type identity. DNA methylation is maintained by three different pathways: CG methylation by DNA METHYLTRANSFERASE 1 (MET1), CHG methylation by CHROMOMETHYLASE (CMT3), a plant specific DNA methyltransferase, and asymmetric CHH methylation through de novo methylation by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) (Law & Jacobsen, 2011).  Although in most cases DNA methylation is a stable epigenetic mark, reduced levels of methylation are observed during plant development. The loss of methylation can either occur passively, via replication in the absence of 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 methylation imprint present in the parental DNA suggesting their role in stress protection memory(Suzuki & Bird, 2008). On the contrary, the asymmetrical cytosine methylation must be reestablished de novo after each replication cycle. Even though genes involved in DNA repair or epigenetic regulation of transcription have been studied extensively in plants evidence for components linking DNA repair and epigenetic inheritance is poorly known. DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin (Pikaard et al., 2014; Zamir, 2001). For this reason, it has been proposed that MET1 and DDM1 are involved in DNA damage response (Shaked, Avivi-ragolsky, & Levy, 2006). Showing that DDM1 mutations, generates a strong alteration in nuclear organization and chromatin structure, particularly in the centromeric and pericentromeric regions resulting in the impediment of DNA repair machinery to not have access to the damaged sequences. This fact emphasizes the broad involvement of recombination and repair DNA proteins in genome maintenance and link between epigenetic and genetic processes.

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