Transposable element products, functions, and regulatory networks in Arabidopsis thaliana

Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within and across genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated due to difficulties in defining TE genes in genomes. Here, we leveraged extensive long- and short-read transcriptome data, together with structural predictions, transcription factor binding site identification, and transcriptional network analyses, to construct a comprehensive atlas of TE transcripts and TE-encoded products in the model organism Arabidopsis thaliana. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed dozens of hitherto unidentified domains of unknown function, enabling us to predict proteins with multimerization and DNA binding domains forming macromolecular complexes involved in transposition. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive atlas of TE-genes and TE-proteins provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.