Fig. 5

Temporal dynamics of promoter-centric interactions during differentiation. a Temporal changes in gene expression (RNA-seq), chromatin interactions (CAPTURE-3C-seq), chromatin accessibility (ATAC-seq), and epigenetic landscapes (H3K27ac and H3K4me3 ChIP-seq) at the captured activated promoters during erythroid differentiation of G1ER cells. The x-axis denotes the time points of undifferentiated (0 h) or differentiated (2, 6, 12, and 24 h) G1ER cells. The y-axis denotes the normalized signals calculated by the mean normalized gene FPKM (RNA-seq), read counts (ATAC-seq and ChIP-seq), or PETs (CAPTURE-3C-seq) per kilobase of captured genomic region per million mapped reads and shown as mean ± SEM (N = 22 activated promoters). b Temporal changes in gene expression, chromatin interactions, chromatin accessibility, and epigenetic landscapes at the captured repressed promoters during erythroid differentiation of G1ER cells. The y-axis denotes the normalized signals shown as mean ± SEM (N = 20 repressed promoters). c Temporal changes in gene expression and chromatin interactions (all, E-P, and other interactions) at the captured activated promoters during erythroid differentiation. E-P interactions and gene expression were significantly and positively correlated (Pearson correlation coefficient R = 0.890, P = 0.022 by Student’s t test), whereas the other interactions showed no significant correlation (R = 0.698, P = 0.095). d Temporal changes in gene expression and chromatin interactions (all, E-P, and other interactions) at the captured repressed promoters. E-P interactions and gene expression were significantly and positively correlated (Pearson correlation coefficient R = 0.905, P = 0.018), and the other interactions also showed a positive correlation with expression (R = 0.871, P = 0.028). e Top enriched TF motifs at genomic regions associated with E-P interactions or other interactions with the captured activated promoters. f Top enriched TF motifs at the genomic regions associated with E-P interactions or other interactions with the captured repressed promoters. g Chromatin occupancy of GATA1 at enhancers interacting with the captured activated or repressed promoters in undifferentiated (0 h) and differentiated (24 h) G1ER cells. P values were calculated using the two-sample Kolmogorov-Smirnov (K-S) test. h Chromatin occupancy of TAL1 at enhancers interacting with the captured activated or repressed promoters in undifferentiated (0 h) and differentiated (24 h) G1ER cells. i Spatial distribution of chromatin accessibility at the captured activated or repressed promoters, enhancers, and other regions interacting with captured promoters in undifferentiated (0 h) and differentiated (2, 6, 12, and 24 h) G1ER cells. P values were calculated using the two-sample Kolmogorov-Smirnov (K-S) test. ***P < 0.0001, **P < 0.01, *P < 0.05, n.s. not significant. j Spatial distribution of H3K27ac ChIP-seq signals at the captured activated or repressed promoters, enhancers, and other regions interacting with captured promoters in undifferentiated and differentiated G1ER cells