Gene DNA methylation in plants: selective pressures and epigenetic conflicts

Aline Muyle

University of Lyon

Link to seminar: https://umontpellier-fr.zoom.us/webinar/register/WN_2NZUnmt2SFyemOg-VbwoTg

https://faculty.sites.uci.edu/alinemuyle/

A longstanding question is whether epigenetics can play a role in adaptation. We know that, in plants, some epigenetic marks can be transmitted over many generations and accumulate epimutations over time. If these heritable epigenetic marks can affect the fitness of individuals, they could potentially be the target of selection and allow species adaptation just like normal genetic alleles. However, it is difficult to assess the effect of epigenetic marks on fitness due to linked genetic variation. We used a population epigenomics approach relying on the Site Frequency Spectrum (SFS) to infer the intensity of selection acting on DNA methylation. We used the 1001 methylome dataset of Arabidopsis thaliana natural populations. Our work suggests that some genes methylated in the CG context are under selection to remain CG methylated. This selection could be due to an effect of CG gene body methylation on gene expression level.

            Another aspect of epigenetics is its role in the silencing of transposable elements. In plants, this is controlled by siRNAs (small interfering RNAs) that lead to DNA methylation in the three contexts (CG, CHG and CHH, where H stands for A, C or T). It happens that transposable elements capture fragments of gene sequences. Gene fragments are then embedded inside the transposable element. This phenomenon leads to sequence homology between the gene fragment within the transposable element and the gene itself, potentially allowing the targeting of the gene by siRNAs and its silencing. It has been hypothesized that gene capture by transposable elements could mitigate silencing by the host, due to the deleterious effect of silencing its own genes. We tested for this epigenetic conflict model in maize.

Recent publications:

1. Muyle A, Gaut BS. 2019. Loss of Gene Body Methylation in Eutrema salsugineum Is Associated with Reduced Gene Expression. Mol. Biol. Evol. 36:155–158.

2. Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. 2021. Gene capture by transposable elements leads to epigenetic conflict in maize. Mol Plant 14:237–252.

3. Muyle A, Ross-Ibarra J, Seymour DK, Gaut BS. 2021. Gene body methylation is under selection in Arabidopsis thaliana. Genetics. Accepted.