Synthetic deconvolution of an auxin-dependent transcriptional code
How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.
Authors
- Marie‐France Gérentes
- François Parcy (ORCID: https://orcid.org/0000-0003-2191-500X)
- Guillaume Cerutti (ORCID: https://orcid.org/0000-0003-2003-9335)
- Matías D. Zurbriggen (ORCID: https://orcid.org/0000-0002-3523-2907)
- François Roudier (ORCID: https://orcid.org/0000-0002-1757-6386)
- Teva Vernoux (ORCID: https://orcid.org/0000-0002-8257-4088)
- Bruno Guillotin (ORCID: https://orcid.org/0000-0002-0117-2512)
- Coralie Cancé
- Emmanuel Thévenon
- Jérémy Lucas (ORCID: https://orcid.org/0000-0002-2252-4732)
- Raquel Martín-Arevalillo (ORCID: https://orcid.org/0000-0003-0674-0053)
- Renaud Dumas (ORCID: https://orcid.org/0000-0003-1404-3274)
- Jonathan Legrand (ORCID: https://orcid.org/0000-0001-7496-3801)
- Annick Dubois (ORCID: https://orcid.org/0000-0002-3646-3811)
- Kenneth D. Birnbaum (ORCID: https://orcid.org/0000-0002-8423-6859)
- Alice Hugues
- Carlos S. Galván-Ampudia (ORCID: https://orcid.org/0000-0002-4779-3568)
- Kun Tang (ORCID: https://orcid.org/0000-0002-4796-9869)
- Jonas Schön (ORCID: https://orcid.org/0000-0002-8955-3079)
- Graeme Vissers
- Mohammed Mohammed Ateequr
- Marianne Dreuillet
Institutions
- Université Claude Bernard Lyon 1 (FR)
- École Normale Supérieure de Lyon (FR)
- New York University Abu Dhabi (AE)
- Centre National de la Recherche Scientifique (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- CEA Grenoble (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Laboratoire Physiologie Cellulaire & Végétale (FR)
- Cluster of Excellence on Plant Sciences (DE)
- Laboratoire Reproduction et Développement des Plantes (FR)
- Heinrich Heine University Düsseldorf (DE)
- New York University (US)
- Université Grenoble Alpes (FR)
Publication Details
- Journal
- Cell
- Published
- 2025-04-15
- DOI
- https://doi.org/10.1016/j.cell.2025.03.028
- Citations
- 10
- Primary Topic
- Plant Molecular Biology Research
- Type
- article
- Field-Weighted Citation Impact
- 17.50
Funders
- Human Frontier Science Program
- Deutsche Forschungsgemeinschaft
- Agence Nationale de la Recherche
- HORIZON EUROPE European Research Council