The dynamism of transposon methylation for plant development and stress adaptation

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; thus, the plant gets protected from environmental stresses as a consequence of the alterations. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. The epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes; thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Further, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability, thus introducing novel gene functions and structural variation in the insertion sites and mainly contributing to epigenetic modifications. Altogether indirectly or directly promote the ability of the plants to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major function in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position on plant genome. High-throughput techniques have greatly advanced our understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. Still, application development in this area has been confined, and an integrated view of TE function and subsequent processes is lacking. In this review, we accordingly explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and some recent examples of how TEs impact gene expression for plant development and stress adaptation.