Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis

Abstract

DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Our results are also consistent with CMT3-induced ectopic methylation of promoters or bodies of genes undergoing transcriptional activation reducing their expression. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.

Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes

“…These findings confirm that CMT3 is sloppy and can methylate contexts other than CHG. Methylation changes caused by embryonic CMT3 hyperexpression were maintained over cell divisions and still observed in 3-week-old plants, consistent with the model that CMT3-induced epimutations give rise to gbM that can be maintained by MET1 across cell divisions and generations. The same gene patterns were repeatedly observed in independent transgenic lines, confirming that CMT3 hypermethylation is not stochastic and tends to target a specific gene set ( Papareddy et al 2021 ). CMT3-induced hypermethylation was also enriched in genes characterized by inaccessible chromatin marks and heterochromatin histone variants ( Papareddy et al 2021 ).…”

“…The same gene patterns were repeatedly observed in independent transgenic lines, confirming that CMT3 hypermethylation is not stochastic and tends to target a specific gene set ( Papareddy et al 2021 ). CMT3-induced hypermethylation was also enriched in genes characterized by inaccessible chromatin marks and heterochromatin histone variants ( Papareddy et al 2021 ). Altogether, these observations lead to a model in which gbM establishment is caused by the recruitment of CMT3, the formation of a feedback loop that ultimately produces CHG, CHH, and CG methylation, the eventual removal of CHG and CHH methylation, and the maintenance of the remaining CG methylation by MET1 ( fig.…”

“…The role of CMT3 in genic de novo methylation was recently confirmed in A. thaliana mutants that hyperexpress CMT3 during late embryonic development ( Papareddy et al 2021 ). CMT3 hyperexpression induces embryonic hypermethylation predominantly in the CWG context, but hypermethylation is also found in other contexts, including CG dinucleotides.…”

“…CG, CHG, and CHH DNA methylation are drawn as black, gray, and white lollipops, respectively. ( a and b ) CMT3 induces de novo methylation at CHG sites of genes associated with inaccessible chromatin marks and heterochromatin histone variants ( Papareddy et al 2021 ). ( b and c ) CHG-H3K9me2 self-reinforcing feedback loop is then established.…”

“…This first hypothesis is neutral with respect to selection because it does not assume that gbM has any effect on fitness. Instead, in this scenario, gbM is a consequence of CMT3 activity that is retained and transmitted over generations by MET1 ( Teixeira and Colot 2009 ; Wendte et al 2019 ; Papareddy et al 2021 ).…”