Fig. 4

Dynamic rewiring of promoter-anchored chromatin interactions during trans-differentiation of Pre-B cells to macrophage. a Table shows the number of significant differential interactions when 1h, 12h, and 48h are compared to 0h time point. b Violin plots showing log2 fold changed expression of promoters based on alteration of their contact frequency (decreased and increased) when 1h (decreased = 15, increased = 3), 12 h (decreased = 77, increased = 143), and 48h (decreased = 313, increased = 1011) are compared to 0h time points. A two-sided Mann–Whitney U test is performed for the significance test. c The log2 fold change of gene expression on gene promoters significantly increased and decreased chromatin interactions (48h vs 0h) with histone modification marks. H3K27me3: promoter interacting regions (PIRs) overlap with at least one H3K27me3 peak, but do not overlap with either H3K27ac or H3K4me1. H3K27ac /H3K4me1: promoter interacting regions (PIRs) overlap with at least one either H3K27ac or H3K4me1, but do not overlap with H3K27me3. H3K27ac/H3K4me1 + H3K27me3: promoter interacting regions (PIRs) overlap with at least one either H3K27ac or H3K4me1 and overlap with H3K27me3. Increased: H3K27me3 (n = 74); H3K27ac/H3K4me1 (n = 668); H3K27ac/H3K4me1 + H3K27me3: (n = 299); decreased: H3K27me3 (n = 5); H3K27ac/H3K4me1 (n = 269); H3K27ac/H3K4me1 + H3K27me3 (n = 66). The unpaired two-sided t-test was performed to test significant differences between groups. The unpaired two-sided t-test was performed to test significant differences between groups. d Log2 fold change of gene expression based on the number of H3K27ac peaks on the increased PIRs (48h vs 0h). The number of histone mark peaks is classified into three groups. ≤ 1: Genes that gain chromatin interactions with less than one histone mark peaks (n = 469). 1–5: Genes that gain chromatin interactions with one to five histone mark peaks (n = 229). > 5: Genes that gain chromatin interactions with greater than five histone mark peaks (n = 44). The unpaired two-sided t-test was performed to test significant differences between groups. e Heatmap shows 5640 significantly different interactions clustered based on the Euclidean distance for interaction score (CHICAGO score greater than 5 in at least one of the groups). Group 1 is 48-h specific interactions (n = 2169). Group 2 is 0-h specific interactions (n = 395). f Enriched GO term for genes in Group 1 and Group 2. Top panel—GO terms for genes (n = 1190) involved in 48h specific interactions; lower panel—GO term for genes (n = 656) involved in 0h specific interactions. g Examples of significantly increased interactions at Ccl7 and Ccl12 loci (left panel) and significantly decreased interactions at Suz12 loci (right panel) across time points