Discrete and cell-specific hypoxic responses in Arabidopsis roots resolved by single-nuclei transcriptomics

With the intensification of unpredictable flooding events because of global warming, there is a need to understand how root cells perceive and respond to oxygen deprivation. The use of high-throughput single-nuclei RNA sequencing (snRNA-Seq) allows the examination of gene expression profiles in discrete cell types. Here, root tips segments of Arabidopsis seedlings were subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4h and analyzed by snRNA-Seq. Hypoxia induces a major transcriptome rewiring, most prominent in the meristematic root cells, with the exclusion of the quiescent center (QC), which is vulnerable to low oxygen. Changes in carbon and nitrogen metabolism by low oxygen were centered around increasing demand for carbohydrate to drive substrate phosphorylation via fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aminotransferase upregulation. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen. Overall design: Arabidopsis roots were subjected to 4h of normoxic (21% oxygen) or hypoxic (4% oxygen) conditions. Nuclei were isolated from 1cm root tips and analyzed with snRNA-seq.