Fig. 3

Chromatin 3D structure and chromatin accessibility are correlated upon HS in rice. a Distribution of ATAC peaks around genes and the changes upon HS in Nip and 93-11, respectively. ATAC occupancy was defined as the normalized reads count in ATAC-seq data. p values were calculated by performing the Wilcoxon test. b Distribution of ATAC peaks around genes in A/B compartment and the changes upon HS in Nip and 93-11, respectively. p values were calculated by performing the Wilcoxon test. c Relationship between A/B compartment and differential ATAC peaks. Tables showing the number of differential ATAC peaks in A/B compartment switch regions upon HS in Nip and 93-11, respectively. Odds ratio indicates the strength of the association, and p values that indicate the association significance were calculated by Fisher’s exact test. d Distribution of ATAC peaks around genes in A/B compartment switching regions and the changes upon HS in Nip and 93-11, respectively. e Comparing of the number of differential ATAC peaks between domain with and without (w/o) missed TAD boundary upon HS in Nip and 93-11, respectively. f Distribution of ATAC peaks around TADs and the changes upon HS in Nip and 93-11, respectively. g Example showing the correlation of Hi-C PC1, ATAC signal, and RNA-seq reads upon HS. In 93-11, LOC_Os02g35500 located in the A compartment under normal condition and switched to the B compartment upon heat stress, associated with its reduced ATAC peak and downregulated gene expression. In Nip, LOC_Os02g35500 located in the A compartment under normal and HS condition, and ATAC peak and gene expression were not significantly changed upon HS