biostudies-literatureLiu FNatural Science Foundation of China20https://www.ebi.ac.uk/biostudies/studies/S-EPMC11742292biostudies-literatureUnknown115(1)Various biological processes are interconnected in plants. Transcription factors (TFs) often act as regulatory hubs to regulate plant growth and responses to stress by integrating various biological pathways. Despite extensive studies on TFs functions in various plant species, our understanding of the details of TFs regulation remains limited. In this study, clonal seedlings of Salvia miltiorrhiza were exposed to specific inhibitors for 12 h. Time-series transcriptome data, sampled hourly, were used to construct co-expression networks and gene regulatory networks (GRNs). Transcriptome dynamic analysis was utilized to capture the gene expression dynamics of various biological processes and decipher the potential molecular mechanisms that regulate these processes. The perturbation results shPlant molecular biologyTime-series transcriptome analysis reveals the cascade mechanism of biological processes following the perturbation of the MVA pathway in Salvia miltiorrhiza.PMC1174229282373984Yan ZYChen XLiu FLi NfalseTime-series transcriptome analysis reveals the cascade mechanism of biological processes following the perturbation of the MVA pathway in Salvia miltiorrhiza.Various biological processes are interconnected in plants. Transcription factors (TFs) often act as regulatory hubs to regulate plant growth and responses to stress by integrating various biological pathways. Despite extensive studies on TFs functions in various plant species, our understanding of the details of TFs regulation remains limited. In this study, clonal seedlings of Salvia miltiorrhiza were exposed to specific inhibitors for 12 h. Time-series transcriptome data, sampled hourly, were used to construct co-expression networks and gene regulatory networks (GRNs). Transcriptome dynamic analysis was utilized to capture the gene expression dynamics of various biological processes and decipher the potential molecular mechanisms that regulate these processes. The perturbation results sh2025-01-01T00:00:00Z2025 Jan2026-07-15T08:54:15.255Z2025-04-05T11:18:10.578ZS-EPMC117422923982183810.1007/s11103-024-01547-5