Borreda, C. | bioRxiv Science

bioRxiv2026

Evolution of transposons as controlling elements

Transposons were originally described as controlling elements, yet the molecular basis and evolutionary origin of their transcriptional regulatory activities remain elusive. Here, we show that transcriptional regulatory activity is an intrinsic property of transposases (TPases). We demonstrate that the Arabidopsis AtMu1 TPase is sufficient to induce sequence-specific transcriptional activation of cognate copies, revealing a pre-existing cis-regulatory network. We further demonstrate that long-recognized Spm transposon-encoded transcriptional regulator TnpA evolved from an ancestral TPase, linking transcriptional regulators to TPases. Across eukaryotes, we identify multiple domesticated TPase-derived proteins that recurrently lack catalytic residues for transposition, consistent with a one-step regulatory co-option through loss of catalytic activity. Together, our results reveal TPases as autonomous sequence-specific transcriptional regulators and provide a direct evolutionary route from TPases to transcription factors.

genetics↗

bioRxiv2024

Transposable element products, functions, and regulatory networks in Arabidopsis

Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated. Here, we leveraged extensive long-and short-read transcriptome data, structural predictions, and regulatory networks analyses, to construct a comprehensive atlas of TE transcripts and their 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 hitherto unidentified domains, uncovering proteins with multimerization and DNA binding domains forming macromolecular complexes. 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 functional atlas provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.

genomics↗