Integrated ATAC-seq and RNA-seq reveal RcHSF30 regulating sHSP and BAG for thermotolerance in rose

High temperatures significantly hinder the application of roses in landscaping and negatively impact floral yield and quality. However, the transcriptional regulatory network governing the heat stress response (HSR) in roses remains poorly understood. In this study, ATAC-seq and RNA-seq profiling of Rosa chinensis under heat stress revealed dynamic changes in chromatin accessibility within two hours of exposure. Differentially accessible regions (DARs) were found to be downregulated in promoters but upregulated in intergenic regions. Heat-activated genes associated with upregulated DARs were enriched in pathways related to stress resilience across four timepoints. Notably, heat-responsive genes harbored abundant heat shock factor (HSF) binding motifs within their accessible regions. The small heat shock protein gene ( HSP18.1 ) and Bcl-2-associated athanogene gene ( BAG6 ) showed strongest chromatin accessibility-expression correlations, containing HSF cis-elements in their promoters. We identified RcHSF30 (a member of the HSFA2 family) as significantly upregulated during heat stress. Molecular docking analysis and electrophoretic mobility shift assays (EMSA) confirmed that RcHSF30 binds to the accessible promoter regions of RcHSP18.1 and RcBAG6 . Overexpression of RcHSF30 in transgenic R. rugosa enhanced thermotolerance, reduced reactive oxygen species (ROS) accumulation, and upregulated the expression of HSP18.1 and BAG6 . This study elucidates the epigenetic regulatory mechanisms underlying the heat stress response in roses and provides a foundation for the development of heat-tolerant rose cultivars. • Heat stress caused a fast shift in chromatin architecture in R. chinensis . • Transcription factors involved in rose heat stress response were screened by ATAC-seq. • Heat stress induced the accessible promoter regions of the HSPs , BAG6 , and antioxidase genes. • RcHSF30 gene was successfully converted into R.rugosa, which may contribute to heat tolerance. • The RcHSF30-RcHSP18.1/BAG6 module was shown to regulate heat tolerance in rose.