Fig. 2: The high-order tomato chromatin organization is strongly affected by heat stress.
a Chromosome 10 Hi-C interaction frequency heatmap at a 100-kb resolution in control and heat stress conditions (1 h). Each pixel denotes all interactions between any to 100 kb genomic loci from the linear genome. Intensity represents log2 normalized contact frequencies. b Averaged scaling plot of interaction frequencies against increasing genomic distance for all tomato pericentromeric regions (gene poor region). The genomic bin size is 100 kb. c Averaged scaling plot of interaction frequencies against increasing genomic distance for all tomato chromosome arms (gene-rich regions). The genomic bin size is 100 kb. d Saddle plots of Hi-C data representing the mean observed interaction frequencies divided by expected interaction frequencies between 20 kb bins. Interactions between A compartments are in the top right, and interactions between B compartments are in the bottom left. e Hi-C interaction heat maps at a 5 kb resolution surrounding a genomic region with differential gene expression along the time course analysis. f Self-organizing map (SOM) of chromatin accessibility profiles at 0, 1 and 6 h of heat stress. Red areas mark over-accessible chromatin sites, blue areas mark under-accessible chromatin sites. g K-means clustering of differentially accessible peaks. h Example of proximal regulatory elements (REs) showing correlation between RNA-seq signals and ATAC-seq signals along the time course. i Correlation between ATAC-seq and RNA-seq data shown by heatmaps of proximal accessible chromatin sites and corresponding gene expression levels. j HOMER DNA-motif enrichment analyses of proximal accessible chromatin peaks. k TF network built by integration of RNA-seq and ATAC-seq data. Source data of Fig. 2g are provided as a Source Data file.
