Transposable elements (TEs) are major drivers of plant genome plasticity, but the immediate molecular consequences of new TE insertions remain poorly understood. In this study, we generated a wild-type Arabidopsis thaliana population with novel insertions of ONSEN retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel ONSEN insertions were distributed non-randomly, with a strong preference for genic regions, particularly in chromatin enriched for H2A.Z, H3K27me3, and H3K4me2. Most full-length ONSEN insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, ONSEN insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new ONSEN copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original ONSEN element, the euchromatic and heterochromatic insertions display distinct methylation signatures, reflecting the action of different epigenetic pathways. In conclusion, our results demonstrate that DNA methylation and alternative splicing are effective control mechanisms safeguarding the plant genome and transcriptome integrity after retrotransposition burst.

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins.

As a result of the accident at the Chornobyl Nuclear Power Plant, significant territories were exposed to ionizing radiation. Some isotopes, such as ¹³⁷Cs, are capable of making a significant impact on living organisms in the long-term perspective. The generation of reactive oxygen species is one mechanism by which ionizing radiation affects living organisms, initiating mechanisms of antioxidant protection. In this article, the effect of increased ionizing radiation on the content of non–enzymatic antioxidants and the activity of antioxidant defense enzymes of Helianthus tuberosum L. was studied. This plant is widely distributed in Europe and characterized by high adaptability to abiotic factors. We found that the activity of antioxidant defense enzymes, such as catalase and peroxidase, weakly correlated with radiation exposure. The activity of ascorbate peroxidase, on the contrary, is strongly positively correlated with radiation exposure. The samples growing on the territory with constant low exposure to ionizing radiation were also characterized by an increased concentration of ascorbic acid and water-soluble phenolic compounds compared to the controls. This study may be useful for understanding the mechanisms underlying the adaptive reactions of plants under prolonged exposure to ionizing radiation.

Long Terminal Repeat (LTR) retrotransposons (LTR-RTEs) comprise up to 90% of some plant genomes and drive genome diversification through their amplification. Novel insertions arise during the final stages of the LTR-RTE life cycle, which depends on both LTR-RTE-encoded proteins and host cellular factors. The LTR-RTE elements require host transcriptional machinery for RNA production, followed by nuclear processing/export, translation, virus-like particle assembly, reverse transcription, and genomic integration. This review addresses the following question: What host proteins promote LTR-RTE transposition in plants? Our analysis of recent literature on host factors and cellular compartments implicated in the retrotransposition cycle reveals the extensive integration of LTR-RTEs into host processes. Nonetheless, the precise mechanisms remain poorly resolved, especially in plants with their rich repertoire of LTR-RTEs. We propose integrating plant mobilomics with transposition reporters, genome editing, synthetic biology, and interactomics to elucidate plant-specific mechanisms.

Transposable elements (TEs) are ubiquitous components of plant genomes that profoundly influence plant diversity, adaptation, and genome structure. Transposition of TEs is primarily suppressed by distinct DNA methylation systems. However, the distribution of DNA methylation at the level of individual TEs in plants remains poorly understood. Here, we address this question by generating per-base cytosine methylation maps of individual long terminal repeat retrotransposons (LTR-RTEs) for the large sunflower (Helianthus annuus L.) and the small Arabidopsis thaliana genomes. A. thaliana was selected as the model species, for which genome-wide DNA methylation profiles have been extensively characterized in prior studies. Our analysis revealed significant heterogeneity in methylation patterns both between and within individual LTR-RTE lineages. We also found that the sunflower genes harboring intact or fragmented LTR-RTE insertions exhibit altered DNA methylation and expression profiles, with intact LTR-RTE insertions enriched in stress-response and regulatory pathways. Our interspecies comparison of DNA methylation patterns indicates that methylation patterns are intrinsic features of LTR-RTE lineages, conserved across diverse plant species but influenced by factors such as insertion age, element length, and proximity to genes. Furthermore, we identified epigenetically distinct clusters of Tork and Athila sunflower elements corresponding to separate phylogenetic clades, suggesting a link between epigenetic regulation and the genetic diversity of plant LTR-RTEs.