Gene body DNA methylation in plants

Abstract

The type, amount, and location of DNA methylation within a gene provides pivotal information on the enzymatic pathway by which it was achieved and its functional consequences. In plants (angiosperms specifically), gene body methylation (gbM) refers to genes with an enrichment of CG DNA methylation within the transcribed regions and depletion at the transcriptional start and termination sites. GbM genes often compose the bulk of methylated genes within angiosperm genomes and are enriched for housekeeping functions. Contrary to the transcriptionally repressive effects of other chromatin modifications within gene bodies, gbM genes are constitutively expressed. GbM has intrigued researchers since its discovery, and much effort has been placed on identifying its functional role. Here, we highlight the recent findings on the evolutionary origin and molecular mechanism of gbM and synthesize studies describing the possible roles for this enigmatic epigenetic phenotype.

FIGURE 1. Stylized patterns and types of genic DNA methylation in land plants

Genes can be categorized into different groups based on enrichment of DNA methylation in exonic sequence, which is deposited by different mechanisms. (a) UM: no enrichment of mCG, mCHG, mCHH; (b) gbM: enrichment of mCG only; (c) TSS: enrichment of mCG only at the TSS; (d) CG/CHG: enrichment for mCG and mCHG; and (e) RdDM: enrichment of mCHH. Additionally, the distribution of DNA methylation across the gene-body is indicative of mechanism and molecular consequences.

FIGURE 2. GbM is dependent on a chromomethylase protein

In the model proposed by [17], (a) rare events where IBM1 fails to remove H3K9me2 leads to (b) recruitment of CMT3 and methylation of CHG sites. (c) Methylation of CHG sites recruits KYP/SUVH4/5/6, di-methylating H3K9, and initiating a reinforcing loop with CMT3 and gbM. (d) and (e) CG sites are methylated by a yet undiscovered mechanism. (f) Subsequently, any CG site methylated will be maintained by MET1. (g) Over time, mCG spreads throughout the gene body.

FIGURE 3. Poly-epialleles between A. thaliana accessions might provide the substrate for adaptive evolution

A gene might “flip” DNA methylation state due to a change in targeting by a DNA methylation pathway. Changes to DNA methylation might be stable for many generations or represent more plastic changes occupying shorter periods of time. This variation could be adaptive, for example, in the face of environmental changes. The figure represents one example of a poly-epiallele (AT2G07680) identified by [37].