Abstract
DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode.
Highlights
Epigenetics has become a key factor to understand mechanisms and pathways involved in regulation of the frequency, rate, or extent of gene expression without changing the DNA sequence
To infer if the reproductive behavior of E. curvula is due to differences in DNA methylation, DNA samples from panicles of plants with different reproductive modes were compared
The first analysis was aimed at inferring the number of Differentially Methylated Positions (DMPs) for the three comparisons (FVS, apomictic vs. sexual (AVS), and apomictic vs. facultative (AVF)) in order to assess the methylation level in each genotype and the methylation contexts more affected by changes in apomictic and sexual plants
Summary
Epigenetics has become a key factor to understand mechanisms and pathways involved in regulation of the frequency, rate, or extent of gene expression without changing the DNA sequence. When epigenetics started to arise as a regulatory mechanism it was described as heritable changes in gene function that cannot be explained by changes in DNA sequence [1]. In plants, epigenetics is a mirror of the evolutionary history since they can exhibit remarkable phenotypic plasticity essential to colonize, grow, and reproduce in unpredictable terrestrial environments [3]. Epigenetic mechanisms are key factors during the temporal and spatial fine-tune regulation of gene expression, enabling plants to survive and reproduce successfully in different environments [4]. The limits between epigenetic and genetic regulations are diffuse and the discussion of the scope of each one is still ongoing. Histone modification and de novo DNA methylation are RNAi-dependent mechanisms; there is a continuous interaction between histone modifications and methylation [5]
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