Fig. 2: Combined RNA-seq and CUT&Tag resolved the regulatory mechanism of PtHSF2.

Gene Ontology (GO) analysis (Level 2) of the top 5 significantly enriched terms for differentially expressed genes (DEGs) between PtHSF2 overexpressing cells and WT cells during the stationary phase at 20 °C. A Biological Process; B Molecular Function; C Cellular Component. The x-axis label “Genes involved (%)” in panels A–C represents the percentage of DEGs associated with a specific GO term within the overlap between the two PtHSF2 overexpressing lines, relative to the total of 1449 DEGs identified. D–F GO analysis of potential target genes identified by CUT&Tag. The x-axis label “Genes involved (%)” in panels D-F indicates the percentage of potential target genes associated with a specific GO term among the 295 target genes identified. G The overlap between the CUT&Tag and RNA-seq, as analyzed in the Venn diagram. H Distribution of CUT&Tag reads around the transcription start site (TSS). IgG, IgG CUT&Tag; PtHSF2, Flag CUT&Tag. I The top three DNA binding motifs of PtHSF2 as revealed by CUT&Tag analysis. CUT&Tag-qPCR was performed to validate the binding sites of PtHSF2, including J the promoter of Cdc45-like; K the promoter of Lhcx2; and L the promoter of ABC. The fold enrichment was normalized to the promoters of β-actin and TBP. IgG (IgG CUT&Tag) and WT (WT CUT&Tag) were used as the control groups. Relative transcription levels of potential target genes (M) Cdc45-like, (N) Lhcx2, (O) ABC, and (P) FAD were determined by qPCR and normalized to β-actin and TBP. J–P Statistical significance was determined using two-tailed unpaired Student’s t-test. Significant difference is indicated at P < 0.05 (*) or P < 0.01 (**) level. Each value represents mean ± SD (n = 3 biological replicates). Source data are provided as a Source Data file.