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Peer-reviewedCC BY-NC-NDNature Communications

A functional atlas of transposon-encoded products and their integration into host networks

  • Carles Borredá1
  • Pol Vendrell‐Mir1
  • Basile Leduque1
  • Mireia Bueno Merino1
  • Céline Oury1
  • Nathalie Glab1
  • Vincent Colot2
  • Leandro Quadrana3
  1. 1Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAe), Université Evry, Université Paris Diderot, Gif sur Yvette, France
  2. 2Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), École Normale Supérieure, PSL Research University, Paris, France
  3. 3Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAe), Université Evry, Université Paris Diderot, Gif sur Yvette, France. [email protected]
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Abstract

Transposable elements (TEs) are pervasive genomic components that propagate via self-encoded factors, yet the nature, regulation, and function of these factors remain largely unresolved. Here, we integrated extensive long- and short-read transcriptome data, regulatory network analyses, deep proteomics, and structural predictions to construct a comprehensive atlas of TE products in Arabidopsis. We show that TE expression is embedded within host regulatory circuits, with DNA methylation and transcription factors jointly shaping TE transcriptional activity. Proteomic analyses confirm the production of over a hundred of high-confidence TE-encoded proteins, and structure-guided analyses of the transcript-informed TE proteome predict previously uncharacterized structural folds, multimerization capacity, and host protein interaction potential. Structural alignments further uncover cryptic homologies between TE-encoded proteins and host factors, including cases of domestications and co-options. Together, our study reveals the functional integration of TEs into cellular pathways and underscores the role of TEs as active drivers of genome function and innovation.

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Cite

BibTeXRIS
BibTeX
@article{borreda2026functional,
  title = {{A functional atlas of transposon-encoded products and their integration into host networks}},
  author = {Carles Borredá and Pol Vendrell‐Mir and Basile Leduque and Mireia Bueno Merino and Céline Oury and Nathalie Glab and Vincent Colot and Leandro Quadrana},
  journal = {Nature Communications},
  year = {2026},
  month = aug,
  doi = {10.1038/s41467-026-76280-2},
  url = {https://doi.org/10.1038/s41467-026-76280-2},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - A functional atlas of transposon-encoded products and their integration into host networks
AU  - Carles Borredá
AU  - Pol Vendrell‐Mir
AU  - Basile Leduque
AU  - Mireia Bueno Merino
AU  - Céline Oury
AU  - Nathalie Glab
AU  - Vincent Colot
AU  - Leandro Quadrana
PY  - 2026
DA  - 2026/08/07
JO  - Nature Communications
DO  - 10.1038/s41467-026-76280-2
UR  - https://doi.org/10.1038/s41467-026-76280-2
AB  - Transposable elements (TEs) are pervasive genomic components that propagate via self-encoded factors, yet the nature, regulation, and function of these factors remain largely unresolved. Here, we integrated extensive long- and short-read transcriptome data, regulatory network analyses, deep proteomics, and structural predictions to construct a comprehensive atlas of TE products in Arabidopsis. We show that TE expression is embedded within host regulatory circuits, with DNA methylation and transcription factors jointly shaping TE transcriptional activity. Proteomic analyses confirm the production of over a hundred of high-confidence TE-encoded proteins, and structure-guided analyses of the transcript-informed TE proteome predict previously uncharacterized structural folds, multimerization capacity, and host protein interaction potential. Structural alignments further uncover cryptic homologies between TE-encoded proteins and host factors, including cases of domestications and co-options. Together, our study reveals the functional integration of TEs into cellular pathways and underscores the role of TEs as active drivers of genome function and innovation.
SN  - 2041-1723
ER  -