Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
Highlights
DNA methylation is an epigenetic mark conserved across various kingdoms in the tree of life
The study of cytosine methylation marks has demonstrated how gene transcription can be fine-tuned beyond the genetic level of control
DNA methylation plays a pivotal role in the suppression of Transposable Element (TE) mobilization to control highly mutagenic TEs from disrupting the essential genes and ensuring the optimal plant fitness
Summary
DNA methylation is an epigenetic mark conserved across various kingdoms in the tree of life. As found in A. thaliana, naturally occurring epialleles serve diverse biological functions in other plant species, a classical example being epiallelic and transcriptional variations in the Lcyc gene in L. vulgaris that controls floral symmetry and the pericarp color (p1) locus in maize, which controls the kernel development and pigmentation [24,25] Such epialleles are involved in the regulation of the ripening and vitamin E accumulation in the fruits of tomatoes [19,20], sex determination and development of flowers in melons [21], and plant architecture and photosynthesis capacity in rice [22,23]. The parental allele-specific transcription of these genes is tightly regulated, and an imbalanced expression can result in strong developmental phenotypes, such as delayed flowering and altered seed sizes [17,42]
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