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Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

ABSTRACT: Plant photomorphogenesis is a light-induced developmental switch combining rapid enrichment in RNA Polymerase II activity and massive gene expression reprogramming. Yet, all former transcriptome analyses of this transition detected no average tendency toward gene upregulation. By applying a spike-in RNA-seq approach, we solved this conundrum and reconciled transcriptome dynamics with epigenomic and cytogenetic data. This further unveiled that Arabidopsis cotyledon photomorphogenesis involves a ~2-fold expansion of the transcriptome, a trend that we reproducibly observed in datasets from independent laboratories upon normalization using a set of stable genes defined ad hoc. This new standpoint enabled us to reinterpret light-mediated gene regulatory paths and unveil a quasi-exclusive positive effect of light-induced transcription factors on target genes. Collectively, this study reveals how environmentally controlled variations of the transcriptional regime can functionally impact plant genome expression. It further establishes a framework for investigating the mechanisms of global genome regulation in these organisms.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE191042 | GEO | 2025/10/16

REPOSITORIES: GEO

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Project description:Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development, however, the mechanism of how they synergistically function is still largely unknown. To explore the underlying mechanisms in photomorphogenesis, genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in presence of light stimuli, or exogenous Brassinolide (BL). Results showed that BR deficiency stimulates, while BL treatment suppresses, the expressions of light responsive genes and photomorphogenesis, revealing the negative effects of BR in photomorphogenesis. This is consistent with that genes involved in cell wall modification and cellular metabolism were specifically modulated by BL during dark-light transition, and altered expressions of genes related to energy utilization. Further analysis revealed that hormone biosynthesis and signaling related genes, especially those of auxin, were altered under BL treatment or light stimuli, indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones. Additionally, suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light, hormone and protein degradation. The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway, which will help to elucidate the molecular mechanism of plant photomorphogenesis. In order to study how BR involves in photomorphogenesis, dark-grown wild-type or BR- deficient mutant det2 seedlings were treated with BL or light, gene expression pattern analysis confirmed that BR deficiency specifically induces, while BL treatment suppresses, the expression of photosynthesis and light responsive genes. Interplay of BR and other hormones play important roles in dark-light transition and photomorphogenesis. CEL files for the wildtype samples are lost. 14 samples were analysised and including repeats.

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Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

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