Single nuclei multiomics reveals the drought-driven gene regulatory atlas in Arabidopsis

The regulation of gene expression in plant responses to drought has been thoroughly investigated in previous studies. Despite this, a detailed understanding of the cell type-specific regulatory mechanisms, encompassing multi-layered biological processes, is lacking. In this study, we report the use of single-nucleus multiomic analysis in Arabidopsis seedlings in response to drought stress. Our single-nuclei RNA (snRNA) analysis delineated 14 distinct clusters representing major root and shoot cell types and discovered new cell type-specific drought markers. Integration of snRNA with single-nuclei ATAC (snATAC) data in leaf epidermis, root endodermis, and guard cells revealed accessible chromatin regions (ACRs)-linked genes predominantly enriched in pathways responsive to drought, heat, and light. Motif enrichment analysis and gene regulatory network (GRN) inference highlighted key transcription factors (TFs) and regulatory networks related to ethylene signaling pathways in endodermis as well as circadian rhythms in both endodermis and guard cells. Pseudotime analysis identified critical transcriptomic progression from metabolic process to stress response within three cell types. Overall, this study elucidates drought-related regulatory mechanisms in Arabidopsis at single-cell resolution, providing valuable insights into the fundamental regulatory events involved in stress responses. It also serves as a reference for future single-cell multiomic investigations in crop plants.