The genome-wide landscape of histone modifications dynamics in non-heading Chinese cabbage root tips under salt stress

• This study constructed a genome-wide modification map of H3K27ac and H3K27me3 in the root tips of NHCC under salt stress. • We found that the root tips of NHCC might respond to salt stress by regulating the cell wall pathway through H3K27ac. • We identified the key gene BcPMEI4 ( pectin methylesterase inhibitor 4 ) of the cell wall pathway with upregulated H3K27ac modification levels in the promoter region under salt stress, and preliminarily verified the positive regulatory effect of BcPMEI4 on salt tolerance of NHCC through VIGS. Non-heading Chinese cabbage (NHCC , Brassica campestris [syn. Brassica rapa ] ssp. chinensis ) is one of the most important leafy vegetables in China. As soil salinization becomes increasingly serious, salt stress limits the growth and development of NHCC, reducing its yield and quality. Previous studies have shown that histone modifications play an important role in plant salt-stress responses by regulating the expression of key genes, but little is known about such modifications in NHCC. Here, we used CUT&Tag-seq and RNA-seq to profile genome-wide H3K27ac and H3K27me3 modifications and transcriptome changes in NHCC root tips subjected to salt stress at 12 and 24 hours. Genome-wide levels of the repressive chromatin mark H3K27me3 increased under salt stress, whereas those of the active chromatin mark H3K27ac decreased. Genes whose H3K27ac and H3K27me3 levels responded to salt stress were associated with processes such as trehalose synthesis, transcription, membrane transport, defense responses, and cell wall structure. Among the cell wall-related genes with increased H3K27ac levels and expression under salt stress, there is a homologous gene of Arabidopsis pectin methylesterase inhibitor 4 ( BcPMEI4 ). The virus-induced gene silencing (VIGS) assay confirmed that silencing BcPMEI4 significantly reduced the salt tolerance of NHCC, as reflected by decreased leaf area, reduced root area, and increased hydrogen peroxide levels. This suggests that the H3K27ac-mediated transcriptional activation of BcPMEI4 may enhance salt tolerance by regulating the cell wall pathway. In summary, our findings provide the comprehensive picture of changes in active and repressive chromatin marks in NHCC under salt stress, offering insight into epigenetic mechanisms of salt-stress response in NHCC and other Brassica crops.