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. Root tip segments of Arabidopsis seedlings subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4 h were 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 glycolytic fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aspartate aminotransferase upregulation. The reduction of nitrate and nitrite in hypoxic cells contributes to amino acid metabolism and the utilization of NO in the phytoglobin-nitric oxide cycle to decrease the redox level and sustain energy production. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen.