Fig. 5: The primed promoter-promoter interaction network may harbor transcription factors.

a A genome-wide promoter-promoter interaction (PPI) map of Arabidopsis for the PPIs present under three temperature conditions was displayed using Cytoscape 3.9.1⁵⁰. The dark pink and purple dots inside the network were two PPI hotspots in chromosomes 2 and 3, respectively. The five individual chromosomes were shown in different colors. The size of the dots indicated the number of PPIs. b An enlarged region of the PPI network on chromosome 2. c Histogram of chromatin contacts over the PPIs across the binding sites of 422 transcription factor (TF). TF binding sites were obtained from previous ChIP experiments^31,52 (see Supplementary Data 2). d Heatmap showing strengths of PPIs across the binding sites of the bHLH, NAC, and WRKY transcription factor families, respectively.