Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis
Plant photomorphogenesis is a light-induced developmental switch that combines massive reprogramming of gene expression and a general enhancement in RNA Polymerase II activity. Yet, transcriptome analyses have failed to demonstrate any tendency toward gene upregulation. To solve this conundrum, we use a spike-in RNA-seq experimental and bioinformatic pipeline, enabling to reconcile transcriptome dynamics with epigenomic and cytogenetic observations of Arabidopsis thaliana cotyledon photomorphogenesis. During the transition, a quasi-unilateral impact of light, with 94% of the differentially expressed genes being upregulated within the first six hours, triggers a two-fold increase in cellular transcript levels. This augmentation of the transcriptome is detected at a similar strength in spike-free RNA-seq datasets re-normalized using stable endogenous transcript levels that mimic the spike-in information. Reanalyzing light-mediated gene regulatory pathways from this standpoint further reveals a quasi-exclusive positive effect of ELONGATED HYPOCOTYL 5 (HY5) and other key light-induced transcription factors on target genes. This study provides a paradigm shift for understanding global genome regulation by light and opens the way to investigate transcriptome size control during other developmentally or environmentally controlled cellular transitions in plants.
Authors
- Célia Baroux (ORCID: https://orcid.org/0000-0001-6307-2229)
- Mickaël Bourge (ORCID: https://orcid.org/0000-0002-4111-6208)
- Frédy Barneche (ORCID: https://orcid.org/0000-0002-7014-7097)
- Delphine Dardalhon-Cuménal
- Geoffrey Schivre (ORCID: https://orcid.org/0000-0001-7644-0422)
- Marie Dumont (ORCID: https://orcid.org/0000-0002-0636-0731)
- Adrien Vidal (ORCID: https://orcid.org/0000-0001-5139-6445)
- M. Davidson (ORCID: https://orcid.org/0000-0003-0881-1409)
- Clara Bourbousse (ORCID: https://orcid.org/0000-0001-6464-6124)
- Léa Wolff (ORCID: https://orcid.org/0009-0003-6362-2085)
- Filippo Maria Mirasole
- Elodie Armanet (ORCID: https://orcid.org/0009-0000-2841-0245)
Institutions
- Centre National de la Recherche Scientifique (FR)
- Inserm (FR)
- Université Sorbonne Nouvelle (FR)
- University of Zurich (CH)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris Sciences et Lettres (FR)
- Université Paris-Saclay (FR)
- Sorbonne Université (FR)
- Institut de Biologie Intégrative de la Cellule (FR)
- Institut de Biologie Paris-Seine (FR)
- Institute of Plant Biology (HU)
- CEA Paris-Saclay (FR)
- Institut de Biologie de l'École Normale Supérieure (FR)
- Développement Adaptation et Vieillissement (FR)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-12-18
- DOI
- https://doi.org/10.1038/s41467-025-66359-7
- Primary Topic
- Light effects on plants
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Velux Stiftung
- Agence Nationale de la Recherche
- Fondation pour la Recherche Médicale
- Centre National de la Recherche Scientifique
- Sorbonne Université