Infographic: Plant Methylation Basics

Multiple molecular mechanisms keep plant DNA methylation in order.

By Jef Akst | February 1, 2017

There are three different types of DNA methylation in plants: CG, CHH (where H is any base except G), and CHG. In Arabidopsis, CG methylation is found on some genes, but primarily on repeat sequences that make up transposons, as well as other repeat sequences in the genome. CHH methylation is found only where there is CG methylation and often near transposable elements, though some evidence points to CHH methylation on some silenced genes as well. CHG methylation is typically found with the CHH variety.



Every time a cell divides, it must replicate its genome and its epigenome. Plants have diverse pathways overseeing the faithful passage of the methylome to daughter cells.

CG methylation
Copying CG methylation patterns to the two daughter strands is relatively straightforward. That’s because this type of methylation is symmetrical: the complementary strand is also CG (reading from 5’ to 3’), and that cytosine is also methylated. So when the parent DNA strand splits, the two daughter strands that form will have methylation on the parent-strand side, and that methylation can guide the addition of a methyl group to the newly replicated strands’ CG cytosine as DNA is being copied.


CHH methylation
CHH methylation is inherently asymmetrical, because the H is any base except guanine. CHH methylation is passed on to both daughter genomes using a process called RNA-directed DNA methylation, which involves small RNAs that guide RNA interference machinery to methylate complementary regions of DNA.


CHG methylation
Although CHG methylation is symmetrical and thus could in principle use the same methylation maintenance pathway as CG methylation, it also relies on RNA-directed DNA methylation (not pictured below). In addition, this type of methylation is paired with methylation of lysine 9 on histone H3 (H3K9). The histomethyltransferase that methylates H3K9 regions binds to methylated CHG. Conversely, the CHG-methylating enzyme binds to H3K9, then methylates nearby CHG sites, forming a positive feedback loop between the two types of methylation.



Arabidopsis pollen grains have three haploid cells: one vegetative cell that helps produce the pollen tube and two sperm. One sperm fertilizes the egg to make the
embryo, while the other fuses with the female’s central cell to form the supportive tissue
known as endosperm.


During reproduction, certain types of DNA methylation are reprogrammed in the pollen.


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