DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst in Arabidopsis thaliana

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 <i>Arabidopsis thaliana</i> population with novel insertions of <i>ONSEN</i> retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel <i>ONSEN</i> 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 <i>ONSEN</i> insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, <i>ONSEN</i> insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new <i>ONSEN</i> copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original <i>ONSEN</i> 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.