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<p>Single-cell sequencing (scRNA-seq) is transforming our ability to dissect cell type-specific gene regulatory networks underlying developmental processes and cellular differentiation with unprecedented resolution. By leveraging single-cell transcriptomes of <i>Arabidopsis thaliana</i> shoot and root apical meristems, we aimed to dissect the complex spatiotemporal interplay between stem cell identity and hypoxia. Single-cell transcriptomic profiling demonstrated a substantial overlap between hypoxia-responsive gene expression and stem cell markers across shoot and root meristems. Trajectory inference coupled with RNA velocity revealed that hypoxia-related transcriptional signatures are enriched in undifferentiated stem cells and gradually decline as differentiation progresses, supporting a critical role for hypoxia in cell fate determination. Our findings suggest that the activation of hypoxia signaling may be a conserved feature in the shoot and root apical meristems of <i>Arabidopsis thaliana</i> and could play a crucial role in regulating stem cell fate decisions during development.</p>

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Inferring hypoxia-responsive regulators of cell fate in plant meristems through single-cell transcriptomics

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月7日

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  • Simone Castellana,
  • Francesco Fioriti,
  • Margherita Marazzini,
  • Francesco Cardarelli,
  • Elena Loreti,
  • Pierdomenico Perata,
  • Paolo Maria Triozzi

摘要

Single-cell sequencing (scRNA-seq) is transforming our ability to dissect cell type-specific gene regulatory networks underlying developmental processes and cellular differentiation with unprecedented resolution. By leveraging single-cell transcriptomes of Arabidopsis thaliana shoot and root apical meristems, we aimed to dissect the complex spatiotemporal interplay between stem cell identity and hypoxia. Single-cell transcriptomic profiling demonstrated a substantial overlap between hypoxia-responsive gene expression and stem cell markers across shoot and root meristems. Trajectory inference coupled with RNA velocity revealed that hypoxia-related transcriptional signatures are enriched in undifferentiated stem cells and gradually decline as differentiation progresses, supporting a critical role for hypoxia in cell fate determination. Our findings suggest that the activation of hypoxia signaling may be a conserved feature in the shoot and root apical meristems of Arabidopsis thaliana and could play a crucial role in regulating stem cell fate decisions during development.