Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution

Abstract

DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.

Keywords: DNA methylation; environmental adaptations; gene expression; plant epigenetics; plant genomic imprinting.

Figure 1

Specific DNA methyltransferases and demethylases mediate cytosine methylation (red circle) in different sequence contexts. CG, CHG, and CHH methylation are carried out by MET1, CMT3, and CMT2, respectively. DRM2, involved in the RdDM pathway, regulates all sequence context methylation. ROS1, DME, DML2, and DML3 act as demethylases.

Figure 2

Different roles of DNA methylation in plant cells. (A) The promoter DNA methylation (red circle) represses transcription activity and gene expression; (B) methylation of the coding regions generates an inaccessible chromatin structure suppressing the aberrant transcription start site; (C) DNA methylation affects genome stability by silencing transposons and other DNA repeated sequences; (D) chromosome interactions through pericentromeric regions or heterochromatin islands depend on the methylation of these regions; (E) DNA methylation could be involved in the biogenesis of circRNAs; (F) mRNA methylation controls stability, splicing, and processing of the transcript itself. TSS, transcription start site; CTSS, cryptic transcription start site; AT, aberrant transcript; TE, transposable elements.

Figure 3

DNA methylation during plant evolution. The diameter of the colored circles represents the genome size of selected species; the dark slice represents the percentage of repeated sequences, and the intensity of the gray represents the level of global DNA methylation. Across plant evolution, DNA methylation assumes new roles represented by colored rectangles. The TE silencing constitutes the most conserved function of methylation. More recently, novel regulation pathways have emerged.