Fig. 1

Chromatin 3D structure dynamics in response to heat stress in rice Nip and 93-11. a Circos plots of the chromatin 3D structure of Nip (left panel) and 93-11 (right panel) genomes. Seven rings from the outside to inside show genomic positions (outmost, black dots marked centromeres), gene expression FPKM (fragments per kilobase per million mapped reads) value for normal (a) and HS (b) samples, PC1 signal of A compartment (red) and B compartment (blue) for normal (c) and HS (d) samples, and TAD-separation score for normal (e) and HS (f) samples. A map connecting homologous regions of the genome is shown inside the figure. The colored lines link collinearity blocks that represent syntenic regions. b Heatmap of the PC1 scores of the HS-induced compartment switching regions in Nip and 93-11, respectively. c Global compartment numbers divided by stable (A-A and B-B) and switching (A-B and B-A) compartments upon HS in Nip and 93-11, respectively. d PC1 scores for chromosome 6 of 93-11, green boxes highlight regions transitioning from A to B and B to A upon HS. e Venn diagram showing the number of shared and sample-specific TADs in Nip and 93-11, respectively. The shared TADs were defined when 80% of the TAD were overlapped. f Boxplot comparing TAD size between normal and HS samples in Nip and 93-11, respectively. g In the regions that lost TAD boundaries upon HS, pie plot showing local compartment numbers divided by stable (A-A and B-B) and switching (A-B and B-A) compartments in Nip and 93-11, respectively. h Example of comparing of Hi-C interaction matrix from a region of chromosome 11 (5-kb resolution) in normal and HS samples in Nip. i Barplot comparing the percentage of different types of interactions between normal and HS samples in Nip and 93-11, respectively. Based on distance, interactions were classified to cis long (> 20 kb) and cis short (< 20 kb) and trans interactions. j Distance plot of interaction strength changes upon HS in Nip and 93-11, respectively