The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Abstract

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These 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. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role 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 in the plant genome. High-throughput techniques have greatly advanced the 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. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants

“…In plants and animals, different forms of stress are known to act as triggers or facilitators of TE mobility [140,141]. Several studies in plants have reported overexpression of TEs following abiotic or biotic stress conditions such as temperature, nitrate de-privation, and wounding [142][143][144][145]. Activation of TEs in response to different stresses has also been demonstrated in insects [146], and especially in the context of insecticide resistance [147][148][149].…”

Differences by origin in methylome suggest eco‐phenotypes in the kelp Saccharina latissima

“…As the genome of Saccharina latissima remains unpublished as of now, we mapped the high-quality reads to the genome of the closely related species Saccharina japonica (Fan et al, 2020;v6.2 from ORCAE (Sterck et al, 2012)). The 476,161,873 trimmed reads (All TrimmedReads, Table S1) were mapped with the SOAP aligner (v1.11, Li et al, 2008) to 548,536,073 in silico digested MethylRAD tags (1,793,114 with CCGG recognition sites,527,987 CCTGG,496,183 CCTGT and 527,729 CCAGG) that we had extracted from the S. japonica genome with a custom python script InSilicoTypeIIbDigestion_corrected.py (https://gist.github.com/alj19 83/a1bcb950013d8ffac9a7fb9ceb70b1c0). For mapping, we used the following specifications: two mismatches allowed (-v 2), sanger quality +33 (-z!…”

Role of Transposable Elements in Genome Stability: Implications for Health and Disease

“…Several studies have suggested that TEs are involved in critical physiological functions such as regulation of stem cell properties, epithelial to mesenchymal transition, inflammation, and many more biological functions [ 40 ]. Evidence also suggests that TEs in mammals have contributed to adaptive characteristics such as increased gene expression, gene replication, and stress tolerance [ 68 ]. Of note, some of the most important physiological contributions are from the TE-derived genes, which in turn participate in a variety of biological functions [ 40 ].…”