Year: 2025
Type: article
Abstract: 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.
Source: Nature Communications
Authors: Geoffrey Schivre, Léa Wolff, Filippo Maria Mirasole, Adrien Vidal, Mhairi L. H. Davidson, Elodie Armanet, Delphine Dardalhon-Cuménal, Marie Dumont, Mickael Bourge, Célia Baroux, Clara Bourbousse, Fredy Barneche
Institutions: Centre National de la Recherche Scientifique, Inserm, Université Paris Sciences et Lettres, Université Paris-Saclay, Institut de Biologie de l'École Normale Supérieure, University of Zurich, Sorbonne Université, Institut de Biologie Paris-Seine, Développement Adaptation et Vieillissement, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Intégrative de la Cellule, CEA Paris-Saclay, École Normale Supérieure - PSL
Language: English
Topic: Light effects on plants
Subfield: Plant Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Awards: Functional links between nuclear architecture and epigenome reprogramming during plant adaptive responses to light, When organelles shape the nucleus: remote control of chromatin architecture by plastid signals, Plant nuclear dynamics in response to light signaling, G4656594441, G4710534001, G7052094829, G7307790887, G7780056158
OpenAlex ID: W4417464609