Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.
Highlights
We will center our following discussion on methylation-related control of transposable elements (TEs) since this mechanism has been widely studied and seems to have a large influence on TE control changes in the genome. We examine how this regulation mechanism influences changes in the genomic landscape of plants, towards potential adaptation and response to different elicitors
Besides TE potential for read-through transcription, gene disruption, generation of intronic sequences and control of gene expression, the epigenetic control of TEs through methylation adds another layer of TE-dependent regulation in the genome
One could think that most mechanisms of silencing established in the genome would point to mitigation of TE spread if these elements are viewed as mere parasites
Summary
The genetic information that modulates the phenotype and that can be inherited without being coded into the DNA sequence is known as epigenetic information. The positioning and spacing of nucleosomes as well as post-translational histone modification, together with DNA methylation, affect the overall packaging of DNA and the accessibility of the transcription unit to specific regulatory elements, which results in altering gene expression [1]. Histone modifications are more diverse and include methylation, phosphorylation, acetylation, ribosylation and ubiquitination of mostly histone H3, but post-translational modifications upon histones H4, H1, and H2A have been described These protein modifications constitute the “histone code” of chromatin epigenetic marks [3]. Regarding RNA-interference mechanisms, small RNAs, together with factors commonly associated with (RNAi) processes, target complementary DNA sequences and recruit factors that can induce chromatin modifications, the formation of heterochromatin, to silence targeted genes [4,5]
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