Gene body methylation is under selection in Arabidopsis thaliana

Abstract

In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM three-fold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype like gene expression.

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

“…For all these reasons, we recently repeated the analyses of Vidalis et al (2016) with the important difference that we separated gbM gene sets from any genes with TE-like methylation ( Muyle et al 2021 ). We also relied on larger data sets—that is, two distinct subsets of 876 and 120 individuals that originated from different sources—from the 1001 methylomes project in A. thaliana ( Kawakatsu et al 2016 ).…”

“…To assess whether selection acts on the gbM state, we characterized the population frequency of methylation at the gene level to estimate the SFS of gene allelic states. Using the population genetic model of Charlesworth and Jain (2014) , we inferred that genes with ancestral gbM in Brassicaceae were under significant selection to remain CG methylated in A. thaliana ( table 1 ; Muyle et al 2021 ) based on the larger data set. Conversely, ancestrally unmethylated genes in Brassicaceae were under selection to remain unmethylated in A. thaliana .…”

“…The former had similar trends as the larger data set but without a significant effect of gbM, and the latter corroborated our gene-level analyses. That is, the overall impression is that CG sites within ancestrally gbM genes in Brassicaceae have been under selection to remain methylated in A. thaliana , while CG sites within ancestrally unmethylated genes have been under selection to be unmethylated in A. thaliana ( Muyle et al 2021 ). Importantly, the results were also confirmed after splitting the gene sets into CHG-gain and non-CHG-gain genes, as characterized by Wendte et al (2019) , showing that biases in epimutation rates between gene sets were not completely responsible for the inferred selection acting on gbM.…”

“…It is worth noting that this species may be atypical in at least three respects. First, two independent studies relying on different data sets and approaches have inferred that A. thaliana has lost gbM three times faster than gaining it ( Takuno et al 2017 ; Muyle et al 2021 ) relative to closely related outcrossing species. Second, the recent shift of A. thaliana to an inbreeding mating system reduced its effective population size ( Mattila et al 2020 ), which is likely to have weakened the efficacy of selection on gbM in that species.…”

“…It is worth emphasizing, however, that this approach, like most comparative approaches, cannot determine causality. More recently, we used the 876 A. thaliana methylomes to study the association between gbM and gene expression within a species by comparing the methylation state of alleles both to their expression level and to the variability in expression across the larger data subset of 876 A. thaliana methylomes ( Muyle et al 2021 ). Across genes with polymorphic methylation states, the expression of gbM alleles was consistently and significantly higher than unmethylated alleles ( table 1 ).…”