Integration of ATAC-seq and RNA-seq unveils transcription factors involved in low-nitrogen tolerance in cucumber

Introduction Nitrogen (N) availability is one of the major factors limiting cucumber ( Cucumis sativus L. ) growth and productivity. However, the hierarchical transcriptional and chromatin-based mechanisms underlying low-nitrogen (LN) adaptation remain unclear. Methods This study investigated the dynamic molecular responses to LN stress and identified key regulatory factors by integrating time-course RNA-seq and ATAC-seq analyses in a tolerant accession (C52) and a sensitive accession (C13). Results LN treatment induced distinct physiological and transcriptional responses: C52 activated a robust "resource-recycling" system, whereas C13 exhibited global chromatin tightening. We identified the bZIP transcription factor CsTGA7 as a core regulator. Functional validation using VIGS demonstrated that CsTGA7 is essential for LN tolerance, maintaining nitrate homeostasis and sustaining stress-responsive gene expression. Discussion These findings provide new insights into the chromatin accessibility-mediated regulation of LN responses and identify CsTGA7 as a promising target for breeding low-nitrogen-tolerant cultivars.