Fig. 2: Chromosomal features of the regulatory circuit.

a TFBSs were grouped according to the number of bound TFs. For each group, the average chromatin openness characterized by the DNase I hypersensitive site (DHS), the regulatory element activity characterized by the H3K9ac read density, and the sequence conservation across four wheat species with different ploidy levels are presented (see Methods). The average signal densities and conservation scores are indicated at a 100-bp resolution within a 10-kb window centered on the merged TFBS centers. Merged TFBSs with more than 12 binding sites were defined as high-occupancy target (HOT) regions. b Fractions of HOT and non-HOT regions overlapping subgenome-homoeologous regions and subgenome-specific regions, which were defined on the basis of the reciprocal alignment across subgenomes (see Methods). c Outer: Circos plot presenting the genomic distribution of gene density as well as HOT and non-HOT regions. Inner: cumulative fractions of the distance between a gene transcription start site and HOT regions or non-HOT regions. d Enrichment of HOT and non-HOT regions in the topologically associating domain (TAD) boundaries (TAD-b), TAD internal regions (TAD-i), and non-TAD regions, which are illustrated above the bar plot, with the fraction of TAD-b, TAD-i, and non-TAD in the genome as the background, respectively. e Genomic tracks illustrating the targeting of the triad gene TPPG by a subset of TFs. The TAD regions, conservation scores across wheat species with different ploidy levels, TE locations, TF binding profiles, and the typical regulatory epigenetic marks, including H3K27me3, H3K4me3, and H3K9ac, are shown. The TPPG promoters are located in subgenome-homoeologous HOT regions and the TAD boundary. f Regulatory circuit integrating information from the TF-target pairs and co-expression modules. Node colors represent different co-expression modules. Circle and diamond nodes represent high- or median-confidence TFs and non-TFs, respectively. g Enlarged image of nodes. Lines with arrows represent targeted and positive co-expression relationships between TF and genes. Lines without arrows represent co-expression between TF and genes. Source data are provided as a Source Data file.