Fig. 6: Promoter-promoter interactions may facilitate co-regulation of gene expression in response to cold.
a Pearson correlation coefficients of expressions from random gene pairs and PPI connected gene pairs at 22 °C. The Pearson correlation coefficients for gene pairs connected by promoter-promoter interaction (PPI) are significantly higher compared to those for randomly selected genes pairs. Randomly selected gene pairs with the same number and similar distance distribution of the PPI connected gene pairs were built as control groups. Random gene pairs A: random gene pairs with the same number; random gene pairs B: random gene pairs with similar distance distribution of PPI gene pairs. Both random procedures were repeated 1000 times. p < 0.0001, two-sided Spearman’s rank correlation. b A circus plot showed the interactions between the promoters of AT3G41768 (rDNA) and 313 genes in the inner circle. From inner to outside, the second circle (blue) showed the co-downregulation of gene expression between 22 °C and 3-h cold treatment (4 °C). The third circle (red) showed co-upregulation of gene expression between 3-h and 12-h cold treatments (4 °C). The outermost circle displayed the five Arabidopsis chromosomes. c Examples showed PPIs of each gene pair. plaNET-seq profile2 showed the transcriptional level of each gene locus at 22 °C, 3-h, and 12-h cold treatments (4 °C).
