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<p>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 <i>Arabidopsis thaliana</i> 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.</p>

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Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月18日

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  • 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

摘要

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.