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

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.